# HG changeset patch
# User rnateam
# Date 1489442089 14400
# Node ID 162c087399ad22e70e52c1e2e357f68ce7d2addc
# Parent  8297557336b2469d3c7c9ef71f539dca34ce7a8b
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/GSPAN commit f971832d2b34a182314e5201ea6895dd207c5923

diff -r 8297557336b2 -r 162c087399ad fasta2shrep_gspan.xml
--- a/fasta2shrep_gspan.xml	Sat Jan 21 17:25:33 2017 -0500
+++ b/fasta2shrep_gspan.xml	Mon Mar 13 17:54:49 2017 -0400
@@ -1,42 +1,76 @@
 <tool id="gspan" name="fasta_to_gspan" version="0.1">
-	<requirements>
-		<requirement type="package" version="0.1.7">graphclust-wrappers</requirement>
-		<requirement type="package" version="2.1.6">rnashapes</requirement>
-	</requirements>
-	<stdio>
-		<exit_code range="1:" />
-	</stdio>
-	<command>
-		<![CDATA[
-
-	  'fasta2shrep_gspan.pl'  --fasta '$dataFasta' $i_crop_unpaired_ends $i_abstr $i_stacks -t "3=0,5=80" -M $M -c $rel_energy_range -win $wins -shift $shift $u $seq_graph_t --group $group
+    <requirements>
+        <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
+        <requirement type="package" version="2.1.6">rnashapes</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+    <![CDATA[
+        fasta2shrep_gspan.pl
+            --fasta '$dataFasta'
+            $i_crop_unpaired_ends
+            $i_abstr
+            $i_stacks
+            -t '3=0,5=80'
+            -M $M
+            -c $rel_energy_range
+            -win $wins
+            -shift $shift
+            $u
+            $seq_graph_t
+            -group $group
 
-]]>
-	</command>
-	<inputs>
-		<param type="data" name="dataFasta" format="fasta" />
-		<param name="i_stacks" truevalue="-stack" falsevalue="" checked="True"  type="boolean" label="Add stacking information to graphs." help="-stack"/>
-		<param name="i_abstr" truevalue="-abstr" falsevalue=""  type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/>
-		<param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue=""  type="boolean" label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/>
-		<param name="M" type="integer" value="5" size="7" label="Max number of shreps that should be taken per window." help="-M"/>
-		<param name="rel_energy_range" type="integer" value="20" size="7" label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/>
-		<param name="wins" type="text" value="40,150" size="20" label=" A list of window sizes to use" help="comma separated integers"/>
-		<param name="shift" type="integer" value="30" size="7" label="The shift of the window, relative to the window size given inpercent." help="by default 30"/>
-		<param name="u" truevalue="-u" falsevalue="" checked="True"  type="boolean" label="Ignore unstable structures (RNAshapes)" help="-u"/>
-		<param name="seq_graph_t" truevalue="--seq-graph-t" falsevalue="" checked="True"  type="boolean" label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/>
-		<param name="group" type="integer" value="10000" size="7" label="Group size." help="by default 10000"/>
-	</inputs>
-	<outputs>
-		<data name="gspan.zip" format="searchgui_archive" from_work_dir="GSPAN_Outputs/1.group.gspan.bz2" label="gspan zip"  />
-	</outputs>
-	<tests>
-		<test>
-			<param name="dataFasta" value="data.fasta"/>
-			<output name="gspan.zip" file="GSPAN_Outputs/1.group.gspan.bz2" />
-		</test>
-	</tests>
-	<help>
-		<![CDATA[
+    ]]>
+    </command>
+    <inputs>
+        <param type="data" name="dataFasta" format="fasta" label="Input file in FASTA format" />
+        <param name="i_stacks" truevalue="-stack" falsevalue="" checked="True"  type="boolean"
+            label="Add stacking information to graphs." help="-stack"/>
+        <param name="i_abstr" truevalue="-abstr" falsevalue=""  type="boolean"
+            label="Add abstract structure graphs to the single shrep graph instances." help="-abstr"/>
+        <param name="i_crop_unpaired_ends" truevalue="-cue" falsevalue=""  type="boolean"
+            label="Add abstract structure graphs to the single shrep graph instances." help="-cue"/>
+        <param name="M" type="integer" value="5" label="Max number of shreps that should be taken per window." help="-M"/>
+        <param name="rel_energy_range" type="integer" value="20"
+            label=" Relative energy range, i.e. percentage (%) of MFE energy (RNAshapes)" help="-c"/>
+        <param name="wins" type="text" value="40,150"
+            label=" A list of window sizes to use" help="comma separated integers"/>
+        <param name="shift" type="integer" value="30"
+            label="The shift of the window, relative to the window size given inpercent." help="by default 30"/>
+        <param name="u" truevalue="-u" falsevalue="" checked="True" type="boolean"
+            label="Ignore unstable structures (RNAshapes)" help="-u"/>
+        <param name="seq_graph_t" truevalue="-seq-graph-t" falsevalue="" checked="True"  type="boolean"
+            label="Add for each 't #' a graph which contains no structure" help="--seq-graph-t"/>
+        <param name="group" type="integer" value="10000"
+            label="Group size" help="by default 10000"/>
+    </inputs>
+    <outputs>
+        <collection name="gspan_compressed" type="list" label="GSPAN Groups" >
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.bz2$" directory="GSPAN_Outputs" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dataFasta" value="data.fasta"/>
+            <param name="i_stacks" value="True" />
+            <param name="i_abstr" value="False" />
+            <param name="i_crop_unpaired_ends" value="False" />
+            <param name="M" value="5" />
+            <param name="rel_energy_range" value="20" />
+            <param name="wins" value="40,150" />
+            <param name="shift" value="30" />
+            <param name="u" value="True" />
+            <param name="seq_graph_t" value="True" />
+            <param name="group" value="10000" />
+            <output_collection name="gspan_compressed" type="list">
+                <element name="1.group.gspan" file="GSPAN_Outputs/1.group.gspan.bz2"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+    <![CDATA[
 
 **What it does**
 
@@ -84,15 +118,9 @@
 + **group** : Combine/group that number of input seqs into 1 gspan file output name is then '<INT>.group.gspan.bz2'
 
     ]]>
-	</help>
-	<citations>
-		<citation type="doi">10.1093/bioinformatics/bts224</citation>
-		<citation type="bibtex">@article{jan:gie:2015,
-author={Janssen, Stefan and Giegerich, Robert},
-title={The RNA shapes studio},
-journal={Bioinformatics},
-year={2015},
-doi={10.1093/bioinformatics/btu649},
-url={http://bioinformatics.oxfordjournals.org/content/31/3/423.abstract}}</citation>
-	</citations>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts224</citation>
+        <citation type="doi">10.1093/bioinformatics/btu649</citation>
+    </citations>
 </tool>