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add new tour
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‎tour_graphclust_wf.yaml‎

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name: GraphClust workflow
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description: Simple instructions for using GrapClust workflow for clustering RNA sequences
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title_default: "<b>GrapClust</b>"
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steps:
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- title: "<b>A tutorial on GrapClust(Clustering RNA sequences)</b>"
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content: "This tour will walk you through the process of <b>GrapClust</b> to cluster RNA sequences.<br><br>
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Read and Follow the instructions before clicking <b>'Next'</b>.<br><br>
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Click <b>'Prev'</b> in case you missed out on any step."
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backdrop: true
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- title: "<b>A tutorial on GraphClust</b>"
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content: "Together we will go through the following steps:<br>
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<dir>
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<b>
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<li>Data Acquisition</li>
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<li>Calling the Workflow</li>
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<li>Understanding the Output</li>
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</b>
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</dir>"
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backdrop: true
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- title: "<b>Create a new history</b>"
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element: '#history-options-button'
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intro: "Let's start by creating a new history:<br>
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<b>(History options :: Create New)</b>"
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position: "left"
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preclick:
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- '#center-panel'
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- title: "<b>Rename the history</b>"
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element: "#current-history-panel > div.controls"
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intro: "Change the name of the new history to <b>'GrapClust'</b>."
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position: "left"
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- title: "<b>Data Acquisition</b>"
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content: "We will start with a simple small <b>FASTA</b> file.<br><br>
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You will get one FASTA file with RNA sequences that we want to cluster.<br><br>"
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backdrop: true
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- title: "<b>Data Acquisition</b>"
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element: ".upload-button"
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intro: "We will import the FASTA file into into the history we just created.<br><br>
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Click <b>'Next'</b> and the tour will take you to the Upload screen."
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position: "right"
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postclick:
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- ".upload-button"
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- title: "<b>Data Acquisition</b>"
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element: "button#btn-new"
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intro: "The sample training data available on github is a good place to start.<br><br>
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Simply click <b>'Next'</b> and the links to the training data will be automatically inserted and ready for upload.<br><br>
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Later on, when you want to upload other data, you can do so by clicking the <b>'Paste/Fetch Data'</b> button or
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<b>'Choose local file'</b> to upload localy stored file."
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position: "top"
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postclick:
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- "button#btn-new"
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- title: "<b>Data Acquisition</b>"
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element: ".upload-text-content:first"
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intro: "Links Acquired !"
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position: "top"
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textinsert:
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https://github.com/eteriSokhoyan/test-data/raw/master/cliques-low-representatives.fa
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- title: "<b>Data Acquisition</b>"
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element: "button#btn-start"
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intro: "Click on <b>'Start'</b> to upload the data into your Galaxy history."
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position: "top"
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- title: "<b>Data Acquisition</b>"
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element: "button#btn-close"
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intro: "The upload may take awhile.<br><br>
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Hit the <b>close</b> button when you see that the files are uploaded into your history."
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position: "top"
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- title: "<b>Data Acquisition</b>"
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element: "#current-history-panel > div.controls"
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intro: "You've acquired your data. Now let's call the <b>GrapClust Workflow</b>.<br><br>"
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position: "left"
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- title: "<b>Running a Workflow</b>"
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element: 'a[href$="/workflow/list_for_run"]'
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intro: "Click on <b>'All Workflows'</b> to access your saved workflows.<br>"
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position: "right"
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- title: "<b>Running a Workflow</b>"
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element: 'a[href$="/workflow/run?id=1cd8e2f6b131e891"]'
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intro: "Select simple one round iteration workflow <b>GrapClust_1_round</b>.<br><br>"
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position: "top"
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- title: "<b>Running a Workflow</b>"
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element: "#field-uid-1 > div.btn-group.ui-radiobutton"
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intro: "We skip <b>'History Options'</b> section because we have already created new history, so there is no need to crate a new one.<br><br>"
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position: "top"
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- title: "<b>Running a Workflow</b>"
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element: "#uid-23 > div.portlet-header > div.portlet-title > span > b"
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intro: "<b>Step 1</b> is the first step of our workflow.Here we should define out input dataset,
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which will be the uploaded FASTA file.<br><br>"
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position: "right"
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- title: "<b>Running a Workflow</b>"
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element: 'button#uid-11'
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intro: "To run the workflow with <b>default setting</b> simply click on <b>'Run workflow'</b> button
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on the top.<br><br>"
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position: "left"
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- title: "<b>Understanding the Output</b>"
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intro: "Running the workflow might take a while.
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After all the steps are done in <b>History panel</b> we will see the outputs.<br><br>"
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position: "top"
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- title: "<b>Understanding the Output</b>"
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element: "#current-history-panel"
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intro: "<b>'cluste.final.stat'</b> file contains general information about clusters,
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e.g. number of clusters, number of sequences in each cluster etc.
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<br> By clicking on the <b>'eye'</b> icon you can see the content of the file.
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<br><br>"
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position: "left"
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- title: "<b>Understanding the Output</b>"
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element: "#current-history-panel"
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intro: "<b>'CLUSTERS'</b> dataset collection contains one file for each cluster. <br>
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Each file contains information about sequences in that cluster. Each line in the file contains:
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<dir>
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<b>
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<li>cluster number</li>
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<li>cm_score</li>
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<li>sequence origin (whether it comes from model or from Infernal search)</li>
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<li>sequence id</li>
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</b>
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</dir>"
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position: "left"
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- title: "<b>A tutorial on GrapClust workflow</b>"
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intro: "Thank You for going through our tutorial."
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backdrop: true

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