Mercurial > repos > proteore > proteore_reactome

annotate reactome_analysis.xml @ 0:216bd2a75b1d draft

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author proteore
date Sun, 26 Nov 2017 19:29:17 -0500
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1 <tool id="reactome_analysis" name="Reactome Analysis Tools" version="0.1.0">
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2 <description>query Reactome with your IDs list
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3 </description>
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4 <requirements>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 #if $opt.input == "text"
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11 python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash"
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12 #else if $opt.input == "file"
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13 python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash"
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14 #end if
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15
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16 ]]></command>
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17 <inputs>
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18 <conditional name="opt">
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19 <param name="input" type="select" label="Input identifiers" multiple="False" >
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20 <option value="text">Copy/paste your list of IDs </option>
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21 <!--option value="file">Choose a single-column file </option-->
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22 <option value="file">Choose a multiple-columns file </option>
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23 </param>
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24 <when value="text" >
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25 <param name="list" type="text" label="Enter list of identifiers" />
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26 </when>
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27 <!--when value="file" >
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28 <param name="idfile" type="data" format="txt" label="Choose a single-column file" />
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29 </when-->
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30 <when value="file" >
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31 <param name="file" type="data" format="txt, tabular" label="Choose a multiple-columns file" help="Input file is a tab-delimited file containing different information of proteins, such as an output of MaxQuant software" />
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32 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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33 <param type="text" name="ncol" value="c1" label="Please specify the column where you would like to apply the comparison" help ='For example, fill in "c1" if you want to filter the first column' />
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34 </when>
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35
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data name="output" format="html" label="" />
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40 <data name="trash" format="tabular" label="Invalid identifiers" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <conditional name="opt" >
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45 <param name="input" value="mq" />
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46 <param name="file" value="UnipIDs.txt" />
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47 <param name="header" value="false" />
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48 <param name="ncol" value="c1" />
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49 </conditional>
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50 <output name="output" file="reactome_output.html" ftype="html" />
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51 <output name="trash" file="reactome_invalide_ids.txt" ftype="tab" />
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 Reactome software provides service of creating diagram representing the relations between the biological processes. This tool allows linking to Reactome web service with pre-loaded data from a list of IDs, a file containing IDs or from a column of a complexed file.
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56
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57 **For the rows that have more than 1 ID, only the first one is taken into account**
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58
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59 **This tool only accepts letters (a-z or A-Z), numbers (0-9) and 3 characters "." "-" "_" for IDs. If there is ID containing other than these characters, it will be removed from the queue and placed in "Invalid identifiers" file**
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60 ]]></help>
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61 <citations>
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62 </citations>
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63 </tool>