Mercurial > repos > proteore > proteore_reactome
comparison reactome_analysis.xml @ 0:216bd2a75b1d draft
planemo upload commit abb24d36c776520e73220d11386252d848173697-dirty
| author | proteore |
|---|---|
| date | Sun, 26 Nov 2017 19:29:17 -0500 |
| parents | |
| children | 35cd50b8ccf2 |
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| -1:000000000000 | 0:216bd2a75b1d |
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| 1 <tool id="reactome_analysis" name="Reactome Analysis Tools" version="0.1.0"> | |
| 2 <description>query Reactome with your IDs list | |
| 3 </description> | |
| 4 <requirements> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 #if $opt.input == "text" | |
| 11 python $__tool_directory__/reactome_analysis.py --json "$opt.list" "list" --output "$output" --trash "$trash" | |
| 12 #else if $opt.input == "file" | |
| 13 python $__tool_directory__/reactome_analysis.py --json "$opt.file" "file" $opt.header $opt.ncol --output "$output" --trash "$trash" | |
| 14 #end if | |
| 15 | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <conditional name="opt"> | |
| 19 <param name="input" type="select" label="Input identifiers" multiple="False" > | |
| 20 <option value="text">Copy/paste your list of IDs </option> | |
| 21 <!--option value="file">Choose a single-column file </option--> | |
| 22 <option value="file">Choose a multiple-columns file </option> | |
| 23 </param> | |
| 24 <when value="text" > | |
| 25 <param name="list" type="text" label="Enter list of identifiers" /> | |
| 26 </when> | |
| 27 <!--when value="file" > | |
| 28 <param name="idfile" type="data" format="txt" label="Choose a single-column file" /> | |
| 29 </when--> | |
| 30 <when value="file" > | |
| 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" /> | |
| 32 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> | |
| 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' /> | |
| 34 </when> | |
| 35 | |
| 36 </conditional> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data name="output" format="html" label="" /> | |
| 40 <data name="trash" format="tabular" label="Invalid identifiers" /> | |
| 41 </outputs> | |
| 42 <tests> | |
| 43 <test> | |
| 44 <conditional name="opt" > | |
| 45 <param name="input" value="mq" /> | |
| 46 <param name="file" value="UnipIDs.txt" /> | |
| 47 <param name="header" value="false" /> | |
| 48 <param name="ncol" value="c1" /> | |
| 49 </conditional> | |
| 50 <output name="output" file="reactome_output.html" ftype="html" /> | |
| 51 <output name="trash" file="reactome_invalide_ids.txt" ftype="tab" /> | |
| 52 </test> | |
| 53 </tests> | |
| 54 <help><![CDATA[ | |
| 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. | |
| 56 | |
| 57 **For the rows that have more than 1 ID, only the first one is taken into account** | |
| 58 | |
| 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** | |
| 60 ]]></help> | |
| 61 <citations> | |
| 62 </citations> | |
| 63 </tool> |