Mercurial > repos > rnateam > graphclust_cmfinder
diff cmFinder.xml @ 4:75c7279ef6f1 draft
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CMFinder commit f971832d2b34a182314e5201ea6895dd207c5923
| author | rnateam |
|---|---|
| date | Mon, 13 Mar 2017 18:01:26 -0400 |
| parents | 271d673b9aef |
| children | 511da75c73be |
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--- a/cmFinder.xml Mon Feb 27 12:01:51 2017 -0500 +++ b/cmFinder.xml Mon Mar 13 18:01:26 2017 -0400 @@ -1,59 +1,61 @@ <tool id="cmFinder" name="cmfinder" version="0.1.0" > - <requirements> - <requirement type="package" version="0.1.9">graphclust-wrappers</requirement> - <requirement type="package" version='0.2'>cmfinder</requirement> - <requirement type="package" version='2.2.10'>viennarna</requirement> - </requirements> - <stdio> - <exit_code range="1:" /> - </stdio> - <command> - <![CDATA[ - - python '$__tool_directory__/cmFinder.py' '$model_tree_stk' '$cmfinder_fa' '' - $gap_threshold_opts.gap_threshold_opts_selector - #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g': - $gap_threshold_opts.gap - #end if + <requirements> + <requirement type="package" version="0.1.10">graphclust-wrappers</requirement> + <requirement type="package" version='0.2'>cmfinder</requirement> + <requirement type="package" version='2.2.10'>viennarna</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ -]]> - </command> - <inputs> - <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" /> - <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" /> - <conditional name="gap_threshold_opts"> - <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help=""> - <option value="--g" selected="true">Yes (--g)</option> - <option value="">No</option> - </param> - <when value="--g"> - <param name="gap" type="float" value="1.0" size="5" + python '$__tool_directory__/cmFinder.py' + '$model_tree_stk' + '$cmfinder_fa' + '' + $gap_threshold_opts.gap_threshold_opts_selector + #if str($gap_threshold_opts.gap_threshold_opts_selector) == '--g': + $gap_threshold_opts.gap + #end if + ]]> + </command> + <inputs> + <param name="model_tree_stk" type="data" format="stockholm" label="model_tree_stk" help="" /> + <param name="cmfinder_fa" type="data" format="text" label="cmfinder_fa" help="" /> + <conditional name="gap_threshold_opts"> + <param name="gap_threshold_opts_selector" type="select" label="Use gap threshold" help=""> + <option value="--g" selected="true">Yes (--g)</option> + <option value="">No</option> + </param> + <when value="--g"> + <param name="gap" type="float" value="1.0" size="5" label="Define the gap threshold to determine the conserved column (--g)" help=""/> - </when> - <when value=""/> - </conditional> - </inputs> - <outputs> - <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/> - </outputs> - <tests> - <test> - <param name="model_tree_stk" value="in.model.tree.stk"/> - <param name="cmfinder_fa" value="cmfinder.fa"/> - <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/> - <param name="gap_threshold_opts.gap" value="1.0"/> - <output name="model_cmfinder_stk" file="model.cmfinder.stk"/> - </test> - </tests> - <help> - <![CDATA[ + </when> + <when value=""/> + </conditional> + </inputs> + <outputs> + <data name="model_cmfinder_stk" format="stockholm" label="model_cmfinder_stk" from_work_dir="model.cmfinder.stk"/> + </outputs> + <tests> + <test> + <param name="model_tree_stk" value="in.model.tree.stk"/> + <param name="cmfinder_fa" value="cmfinder.fa"/> + <param name="gap_threshold_opts.gap_threshold_opts_selector" value="--g"/> + <param name="gap_threshold_opts.gap" value="1.0"/> + <output name="model_cmfinder_stk" file="model.cmfinder.stk"/> + </test> + </tests> + <help> + <![CDATA[ **What it does** At first it converts CLUSTAL format files to STOCKHOLM format. Then using *CMFinder* determines consensus motives for sequences. ]]> - </help> - <citations> + </help> + <citations> <citation type="bibtex">@inproceedings{costa2010fast, title={Fast neighborhood subgraph pairwise distance kernel}, author={Costa, Fabrizio and De Grave, Kurt},