Mercurial > repos > rnateam > graphclust_cmfinder

changeset 4:75c7279ef6f1 draft

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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
files cmFinder.xml
diffstat 1 files changed, 50 insertions(+), 48 deletions(-) [+]
line wrap: on
line diff
--- 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},