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graphclust_very_short.yaml
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graphclust_very_short.yaml
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name: GraphClust workflow fast tutorial
description: Simple and short instructions for using GraphClust workflow for clustering RNA sequences
title_default: "<b>GraphClust_short_tour</b>"
tags:
- "GraphClust"
steps:
- title: "<b>A tutorial on GraphClust(Clustering RNA sequences)</b>"
content: "This tour will walk you through the process of <b>GraphClust</b> to cluster RNA sequences.<br><br>
Read and Follow the instructions before clicking <b>'Next'</b>.<br><br>
Click <b>'Prev'</b> in case you missed out on any step."
backdrop: true
- title: "<b>A tutorial on GraphClust</b>"
content: "Together we will go through the following steps:<br>
<dir>
<b>
<li>Data Acquisition</li>
<li>Calling the Workflow</li>
<li>Understanding the Output</li>
</b>
</dir>"
backdrop: true
- title: "<b>Log in</b>"
element: '#user > li > a'
intro: " To be able to use workflows you should be logged in. So if you already have an account
simply <b>log in</b> or otherwise <b>register</b> by clicking on <b>'User'</b>."
position: "left"
- title: "<b>GraphClust</b>"
intro: "Now when you are logged in we can continue out tour"
position: "left"
backdrop: true
- title: "<b>Data Acquisition</b>"
content: "We will start with a simple small <b>FASTA</b> file.<br><br>
You will get one FASTA file with RNA sequences that we want to cluster.<br><br>"
backdrop: true
- title: "<b>Data Acquisition</b>"
element: ".upload-button"
intro: "We will import the FASTA file into into the history we just created.<br><br>
Click <b>'Next'</b> and the tour will take you to the Upload screen."
position: "right"
postclick:
- ".upload-button"
- title: "<b>Data Acquisition</b>"
element: "button#btn-new"
intro: "The sample training data available on github is a good place to start.<br><br>
Simply click <b>'Next'</b> and the links to the training data will be automatically inserted and ready for upload.<br><br>
Later on, when you want to upload other data, you can do so by clicking the <b>'Paste/Fetch Data'</b> button or
<b>'Choose local file'</b> to upload localy stored file."
position: "top"
postclick:
- "button#btn-new"
- title: "<b>Data Acquisition</b>"
element: ".upload-text-content:first"
intro: "Links Acquired !"
position: "top"
textinsert:
https://github.com/BackofenLab/docker-galaxy-graphclust/raw/master/data/Rfam-cliques-dataset/cliques-low-representatives.fa
- title: "<b>Data Acquisition</b>"
element: "button#btn-start"
intro: "Click on <b>'Start'</b> to upload the data into your Galaxy history."
position: "top"
- title: "<b>Data Acquisition</b>"
element: "button#btn-close"
intro: "The upload may take awhile.<br><br>
Hit the <b>close</b> button when you see that the files are uploaded into your history."
position: "top"
- title: "<b>Data Acquisition</b>"
element: "#current-history-panel > div.controls"
intro: "You've acquired your data. Now let's call the <b>GraphClust Workflow</b>.<br><br>"
position: "left"
- title: "<b>Running a Workflow</b>"
element: 'a[href$="/workflow/list_for_run"]'
intro: "Click on <b>'All Workflows'</b> to access your saved workflows.<br>"
position: "right"
- title: "<b>Running a Workflow</b>"
element: 'a[href$="/workflow/run?id=1cd8e2f6b131e891"]'
intro: "Select simple one round iteration workflow <b>GraphClust_1_round</b>.<br><br>"
position: "top"
- title: "<b>Running a Workflow</b>"
element: "#field-uid-1 > div.btn-group.ui-radiobutton"
intro: "If you want the output to be in a new history click <b>'yes'</b> in <b>'History Options'</b> otherwise just move on.<br><br>"
position: "top"
- title: "<b>Running a Workflow</b>"
element: "#uid-23 > div.portlet-header > div.portlet-title > span > b"
intro: "<b>Step 1</b> is the first step of our workflow.Here we should define out input dataset,
which will be the uploaded FASTA file.<br><br>"
position: "right"
- title: "<b>Running a Workflow</b>"
element: 'button#uid-11'
intro: "To run the workflow with <b>default setting</b> simply click on <b>'Run workflow'</b> button
on the top.<br><br>"
position: "left"
- title: "<b>Understanding the Output</b>"
intro: "Running the workflow might take a while.
After all the steps are done in <b>History panel</b> we will see the outputs.<br><br>"
position: "top"
- title: "<b>Understanding the Output</b>"
element: "#current-history-panel"
intro: "<b>'cluste.final.stat'</b> file contains general information about clusters,
e.g. number of clusters, number of sequences in each cluster etc.
<br> By clicking on the <b>'eye'</b> icon you can see the content of the file.
<br><br>"
position: "left"
- title: "<b>Understanding the Output</b>"
element: "#current-history-panel"
intro: "<b>'CLUSTERS'</b> dataset collection contains one file for each cluster. <br>
Each file contains information about sequences in that cluster. Each line in the file contains:
<dir>
<b>
<li>cluster number</li>
<li>cm_score</li>
<li>sequence origin (whether it comes from model or from Infernal search)</li>
<li>sequence id</li>
</b>
</dir>"
position: "left"
- title: "<b>A tutorial on GraphClust workflow</b>"
intro: "Thank You for going through our tutorial."
backdrop: true