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adjust galaxy wrappers to use scriptmanager_macros
Adjust wrappers to use the tool macros for the scriptmanager jar filename and requirements/dependencies
1 parent a751b2d commit b6171a0

15 files changed

Lines changed: 84 additions & 38 deletions

‎galaxy/wrapper/scriptmanager_aggregate-data.xml‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,14 @@
11
<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>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
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</macros>
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<requirements>
5-
<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_composite-plot.xml‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,14 @@
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<tool id="scriptmanager_composite-plot" name="ScriptManager: Composite Plot"
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version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
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<description> Composite Plot </description>
4-
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
4+
<macros>
5+
<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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</requirements>
710
<command detect_errors="exit_code"><![CDATA[
8-
java -jar $__tool_directory__/ScriptManager-v0.14.jar figure-generation composite-plot
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java -jar $__tool_directory__/@JAR_FILENAME@ figure-generation composite-plot
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#if str($output_file_name.bool) == "Yes" :
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-o "$output_file_name.directory"

‎galaxy/wrapper/scriptmanager_convert-bed-chr-names.xml‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,16 @@
11
<tool id="scriptmanager_convert-bed-chr-names" name="ScriptManager: Convert BED Chr Names"
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version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
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<description> Convert BED Chr Names </description>
4-
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
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<macros>
5+
<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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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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ln -s "$input" "temp_input.bed" &&
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10-
java -jar $__tool_directory__/ScriptManager-v0.14.jar file-utilities convert-bed-genome
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java -jar $__tool_directory__/@JAR_FILENAME@ file-utilities convert-bed-genome
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#if str($output_file_name.bool) == "Yes" :
1316
-o "$output_file_name.file_name"

‎galaxy/wrapper/scriptmanager_convert-gff-chr-names.xml‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,16 @@
11
<tool id="scriptmanager_convert-gff-chr-names" name="ScriptManager: Convert GFF Chr Names"
22
version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> Convert GFF Chr Names </description>
4-
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
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<macros>
5+
<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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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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ln -s "$input" "temp_input.gff" &&
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10-
java -jar $__tool_directory__/ScriptManager-v0.14.jar file-utilities convert-gff-genome
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java -jar $__tool_directory__/@JAR_FILENAME@ file-utilities convert-gff-genome
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#if str($output_file_name.bool) == "Yes" :
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-o "$output_file_name.file_name"

‎galaxy/wrapper/scriptmanager_cross-corr.xml‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,17 @@
11
<tool id="scriptmanager_cross-corr" name="ScriptManager: Cross Correlation"
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version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> BAM Cross Correlation </description>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
6+
</macros>
47
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
8+
<expand macro="requirement_openjdk" />
69
</requirements>
710
<command detect_errors="exit_code"><![CDATA[
811
ln -s "$input" "temp_input.bam" &&
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samtools index "temp_input.bam" &&
1013
11-
12-
java -jar $__tool_directory__/ScriptManager-v0.14-bugfix153.jar bam-statistics cross-corr
14+
java -jar $__tool_directory__/@JAR_FILENAME@ bam-statistics cross-corr
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1416
#if str($output_file_name.bool) == "Yes" :
1517
-o "$output_file_name.file_name"

‎galaxy/wrapper/scriptmanager_filter-bed.xml‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,16 @@
11
<tool id="scriptmanager_filter-bed" name="ScriptManager: Filter Bed"
22
version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> Filter BED by Proximity </description>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
6+
</macros>
47
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
8+
<expand macro="requirement_openjdk" />
69
</requirements>
710
<command detect_errors="exit_code"><![CDATA[
811
ln -s "$input" "temp_input.bed" &&
912
10-
java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis filter-bed
13+
java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis filter-bed
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#if str($output_file_name.bool) == "Yes" :
1316
-o "$output_file_name.file_name"

‎galaxy/wrapper/scriptmanager_filter-pip-seq.xml‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,12 @@
11
<tool id="scriptmanager_filter-pip-seq" name="ScriptManager: Filter Pip Seq"
22
version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> Filter Pip Seq </description>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
6+
</macros>
47
<requirements>
5-
<requirement type="package" version="1.10">samtools</requirement>
6-
<requirement type="package" version="11.0.11">openjdk</requirement>
8+
<expand macro="requirement_openjdk" />
9+
<expand macro="requirement_samtools" />
710
</requirements>
811
<command detect_errors="exit_code"><![CDATA[
912
ln -s "$input1" "temp_input1.fasta" &&
@@ -12,7 +15,7 @@
1215
samtools faidx "temp_input1.fasta" &&
1316
samtools index "temp_input2.bam" &&
1417
15-
java -jar $__tool_directory__/ScriptManager-v0.14.jar bam-manipulation filter-pip-seq
18+
java -jar $__tool_directory__/@JAR_FILENAME@ bam-manipulation filter-pip-seq
1619
1720
#if str($output_file_name.bool) == "Yes" :
1821
-o "$output_file_name.file_name"

‎galaxy/wrapper/scriptmanager_peak-align-ref.xml‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,17 @@
11
<tool id="scriptmanager_peak_align_ref" name="ScriptManager: Align BED to Reference"
22
version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> Align BED to Reference </description>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
6+
</macros>
47
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
8+
<expand macro="requirement_openjdk" />
69
</requirements>
710
<command detect_errors="exit_code"><![CDATA[
811
ln -s "$input_peak" "temp_input_peak.bed" &&
912
ln -s "$input_ref" "temp_input_ref.bed" &&
1013
11-
java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis peak-align-ref
14+
java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis peak-align-ref
1215
1316
#if str($output_file_name.bool) == "Yes" :
1417
-o "$output_file_name.file_name"

‎galaxy/wrapper/scriptmanager_rand-coord.xml‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,14 @@
11
<tool id="scriptmanager_rand-coord" name="ScriptManager: Random Coordinate Generator"
22
version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> Random Coordinate Generator </description>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
6+
</macros>
47
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
8+
<expand macro="requirement_openjdk" />
69
</requirements>
710
<command detect_errors="exit_code"><![CDATA[
8-
java -jar $__tool_directory__/ScriptManager-v0.14.jar peak-analysis rand-coord
11+
java -jar $__tool_directory__/@JAR_FILENAME@ peak-analysis rand-coord
912
1013
"$genome_name"
1114

‎galaxy/wrapper/scriptmanager_randomize-fasta.xml‎

Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,16 @@
11
<tool id="scriptmanager_randomize-fasta" name="ScriptManager: Randomize Fasta"
22
version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
33
<description> Randomize Fasta </description>
4+
<macros>
5+
<import>scriptmanager_macros.xml</import>
6+
</macros>
47
<requirements>
5-
<requirement type="package" version="11.0.11">openjdk</requirement>
8+
<expand macro="requirement_openjdk" />
69
</requirements>
710
<command detect_errors="exit_code"><![CDATA[
811
ln -s "$input" "temp_input.fasta" &&
912
10-
java -jar $__tool_directory__/ScriptManager-v0.14.jar sequence-analysis randomize-fasta
13+
java -jar $__tool_directory__/@JAR_FILENAME@ sequence-analysis randomize-fasta
1114
1215
#if str($output_file_name.bool) == "Yes" :
1316
-o "$output_file_name.file_name"

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