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Merge pull request #171 from CEGRcode/galaxy-wrappers-corepipeline
Complete draft set of galaxy wrappers including ones used for the core pipeline
2 parents 31734cb + b6171a0 commit 2e2f688

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‎.DS_Store‎

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‎galaxy/.DS_Store‎

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‎galaxy/wrapper/.DS_Store‎

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‎galaxy/wrapper/README.md‎

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@@ -45,14 +45,27 @@ sudo git clone https://github.com/CEGRcode/scriptmanager-galaxy_tools.git
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2. Tell galaxy where to look for scriptmanager tools by adding the following section to `/mnt/mountpoint/srv/galaxy/config/local_tool_conf.xml` file.
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```
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<section id="ScriptManager" name="ScriptManager" >
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<tool file="scriptmanager-galaxy_tools/script_manager_heatmap.xml" />
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<tool file="scriptmanager-galaxy_tools/script_manager_tag_pileup.xml" />
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<tool file="scriptmanager-galaxy_tools/scriptmanager_heatmap_add_label.xml" />
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<tool file="scriptmanager-galaxy_tools/script_manager_4color.xml" />
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</section>
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<section id="scriptmanager-owlang" name="ScriptManager" >
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<tool file="scriptmanager-owlang/scriptmanager_bam-correlation.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_bam-to-bed.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_bam-to-bedgraph.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_bam-to-gff.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_bam-to-scidx.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_bed-to-gff.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_expand-bed.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_expand-gff.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_four-color.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_gff-to-bed.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_heatmap.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_label-heatmap.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_merge-heatmap.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_pe-stat.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_se-stat.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_shift-coord.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_sort-bed.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_sort-gff.xml" />
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<tool file="scriptmanager-owlang/scriptmanager_tag-pileup.xml" />
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</section>
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```
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3. Restart Galaxy
@@ -66,3 +79,4 @@ sudo git clone https://github.com/CEGRcode/scriptmanager-galaxy_tools.git
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Thank you to Ali Nematbakhsh(https://github.com/AliNemat) and Audrey Sackey(https://github.com/Adjekai) for their initial work in writing these wrappers.
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‎galaxy/wrapper/macros.xml‎

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‎galaxy/wrapper/scriptmanager_aggregate-data.xml‎

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@@ -1,11 +1,14 @@
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<tool id="scriptmanager_aggregate-data" name="ScriptManager: Aggregate Data"
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version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
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<description> Aggregate Data </description>
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<macros>
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<import>scriptmanager_macros.xml</import>
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</macros>
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<requirements>
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<requirement type="package" version="11.0.11">openjdk</requirement>
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<expand macro="requirement_openjdk" />
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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java -jar $__tool_directory__/ScriptManager-v0.14.jar read-analysis aggregate-data
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java -jar $__tool_directory__/@JAR_FILENAME@ read-analysis aggregate-data
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#if str($output_file_name.bool) == "Yes" :
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-o "$output_file_name.directory"

‎galaxy/wrapper/scriptmanager_bam-correlation.xml‎

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@@ -1,12 +1,12 @@
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<tool id="bamcorrelation_test" name="ScriptManager: BAM Correlation" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
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<tool id="scriptmanager_bam-correlation" name="ScriptManager: BAM Correlation" version="0.1.0" profile="22.01" >
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<description> Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files. </description>
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<requirements>
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<requirement type="package" version="11.0.11">openjdk</requirement>
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<requirement type="package" version="1.9">samtools</requirement>
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</requirements>
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<macros>
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<import>macros.xml</import>
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<import>scriptmanager_macros.xml</import>
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</macros>
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<requirements>
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<expand macro="requirement_openjdk" />
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<expand macro="requirement_samtools" />
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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ln -s '$BAM' bamfile.bam &&
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ln -s '$output1' output1.tab &&
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#end if
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#end if
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java -jar $__tool_directory__/ScriptManager-v0.14-dev.jar bam-statistics bam-correlation
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java -jar $__tool_directory__/@JAR_FILENAME@ bam-statistics bam-correlation
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#if str($read) == "read_1" :
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-1
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#else if str($read) == "read_2" :
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-b "$bin_size"
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--cpu "$cpu"
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'$output1'
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'$output1'
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-t "$tag_shift"
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bamfile.bam
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]]></command>
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<inputs>
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<param type="data" name="BAM" format="bam" multiple="True" label="Input BAM files"/>
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</outputs>
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<help>
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**What it does**
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Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files.
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Genome-Genome correlations for replicate comparisons given multiple sorted and indexed (BAI) BAM files.
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</help>
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</tool>
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<expand macro="citations_pearc" />
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</tool>

‎galaxy/wrapper/scriptmanager_bam-to-bed.xml‎

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<tool id="scriptmanager_bam-to-bed" name="ScriptManager: Convert BAM to BED" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
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<tool id="scriptmanager_bam-to-bed" name="ScriptManager: Convert BAM to BED" version="0.1.0" profile="22.01" >
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<description> Convert BAM file to BED file </description>
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<macros>
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<import>scriptmanager_macros.xml</import>
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</macros>
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<requirements>
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<requirement type="package" version="11.0.11">openjdk</requirement>
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<expand macro="requirement_openjdk" />
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<expand macro="requirement_samtools" />
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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ln -s '$BAM' bamfile.bam &&
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ln -s '$output1' output1.bed &&
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#if $BAM.is_of_type('bam'):
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#if str( $BAM.metadata.bam_index ) != "None":
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ln -s '${BAM.metadata.bam_index}' bamfile.bam.bai &&
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ln -s '$input' bamfile.bam &&
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#if $input.is_of_type('bam'):
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#if str( $input.metadata.bam_index ) != "None":
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ln -s '${input.metadata.bam_index}' bamfile.bam.bai &&
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#else:
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samtools index bamfile.bam bamfile.bai &&
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#end if
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#end if
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java -jar $__tool_directory__/ScriptManager-v0.14.jar bam-format-converter bam-to-bed
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java -jar $__tool_directory__/@JAR_FILENAME@ bam-format-converter bam-to-bed
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#if str($gzip) == "Yes" :
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--gzip
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#end if
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#if str($read) == "read_1" :
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#else if str($read) == "read_2" :
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#else if str($read) == "fragment" :
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-f
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#end if
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#if str($mate_pair) == "Yes" :
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#if str($require_paired_end.mate_pair) == "Yes" :
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-p
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#if str($require_paired_end.filter_by_min.filter_min) == "Yes" :
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-n "$require_paired_end.filter_by_min.min_insert"
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#end if
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#if str($require_paired_end.filter_by_max.filter_max) == "Yes" :
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-x "$require_paired_end.filter_by_max.max_insert"
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#end if
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#end if
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#if str($filter_by_min.filter_min) == "Yes" :
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-n "$filter_by_min.min_insert"
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#end if
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-o output1.bed
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#if str($filter_by_max.filter_max) == "Yes" :
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-x "$filter_by_max.max_insert"
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#end if
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-o '$output'
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bamfile.bam
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]]></command>
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<inputs>
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<param type="data" name="BAM" format="bam" label="Input BAM file"/>
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<param type="data" name="input" format="bam" label="Input BAM file"/>
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<param type="select" name="read" label="Select which read to output">
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<option value="read_1" selected="True" >Read 1</option>
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<option value="read_2" >Read 2</option>
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<option value="combined" >Combined </option>
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<option value="midpoint" >Midpoint (Require PE) </option>
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<option value="fragment" >Fragment (Require PE) </option>
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</param>
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<param type="boolean" name="mate_pair" truevalue="Yes" falsevalue="No" label="Require proper mate-pair" />
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<conditional name="filter_by_min">
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<param type="boolean" name="filter_min" truevalue="Yes" falsevalue="No" label="Filter by min insert size (bp)" >
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</param>
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<conditional name="require_paired_end">
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<param type="boolean" name="mate_pair" truevalue="Yes" falsevalue="No" label="Require proper mate-pair" />
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<when value="Yes">
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<param type="integer" name="min_insert" value="0" label="Min insert size (bp)" />
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</when>
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<when value="No">
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<conditional name="filter_by_min">
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<param type="boolean" name="filter_min" truevalue="Yes" falsevalue="No" label="Filter by min insert size (bp)" />
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<when value="Yes">
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<param type="integer" name="min_insert" value="0" label="Min insert size (bp)" />
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</when>
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<when value="No" />
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</conditional>
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<conditional name="filter_by_max">
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<param type="boolean" name="filter_max" truevalue="Yes" falsevalue="No" label="Filter by max insert size (bp)" />
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<when value="Yes">
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<param type="integer" name="max_insert" value="1000" label="Max insert size (bp)" />
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</when>
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<when value="No" />
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</conditional>
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</when>
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</conditional>
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<conditional name="filter_by_max">
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<param type="boolean" name="filter_max" truevalue="Yes" falsevalue="No" label="Filter by max insert size (bp)" >
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</param>
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<when value="Yes">
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<param type="integer" name="max_insert" value="1000" label="Max insert size (bp)" />
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</when>
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<when value="No">
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</when>
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</conditional>
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<param name="gzip" type="boolean" checked="true" truevalue="Yes" falsevalue="No" label="Gzip output" />
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</inputs>
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<outputs>
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<data name="output1" format="bed" label="${tool.name} (composite) on ${on_string}"/>
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<data name="output" format="bed" label="${tool.name} (composite) on ${on_string}"/>
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</outputs>
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<help>
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**What it does**
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Convert BAM file to BED file.
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**What it does**
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Convert BAM file to BED file.
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</help>
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</tool>
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<expand macro="citations_pearc" />
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</tool>

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