Mercurial > repos > rnateam > graphclust_nspdk

diff NSPDK_sparseVect.xml @ 4:0625db6b6e45 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit f971832d2b34a182314e5201ea6895dd207c5923
author rnateam
date Mon, 13 Mar 2017 18:05:04 -0400
parents d10410cfd17a
children 9b5fb987a484
line wrap: on
line diff
--- a/NSPDK_sparseVect.xml	Mon Feb 27 12:03:12 2017 -0500
+++ b/NSPDK_sparseVect.xml	Mon Mar 13 18:05:04 2017 -0400
@@ -1,39 +1,43 @@
 <tool id="nspdk_sparse" name="NSPDK_sparseVect" version="9.2">
-	<requirements>
-			<requirement type="package" version="0.1.9">graphclust-wrappers</requirement>
-			<requirement type="package" version="9.2">nspdk</requirement>
-	</requirements>
-	<stdio>
-		<exit_code range="1:" />
-	</stdio>
-	<command>
-		<![CDATA[
+    <requirements>
+        <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
+        <requirement type="package" version="9.2">nspdk</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+        <![CDATA[
 
 
-      'NSPDK_sparseVect.pl' '$data_fasta' '$gspan_file'  $max_rad $max_dist_relations
+        NSPDK_sparseVect.pl
+            '$data_fasta'
+            '$gspan_file'
+            $max_rad
+            $max_dist_relations
 
 ]]>
-	</command>
-	<inputs>
-		<param type="data" name="gspan_file" format="searchgui_archive"  />
-		<param type="data" name="data_fasta" format="fasta" />
-		<param name="max_rad" type="integer" value="3" size="5" label="maximum radius " help="-R"/>
-		<param name="max_dist_relations" type="integer" value="3" size="5" label="maximum distance relations" help="-D"/>
-	</inputs>
-	<outputs>
-		<data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/>
-	</outputs>
-	<tests>
-		<test>
-			<param name="data_fasta" value="data.fasta"/>
-			<param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/>
-			<param name="max_rad" value="3"/>
-			<param name="max_dist_relations" value="3"/>
-			<output name="data_svector" file="SVECTOR/data.svector" ftype="zip" />
-		</test>
-	</tests>
-	<help>
-		<![CDATA[
+    </command>
+    <inputs>
+        <param type="data" name="gspan_file" />
+        <param type="data" name="data_fasta" format="fasta" />
+        <param name="max_rad" type="integer" value="3" label="maximum radius " help="-R"/>
+        <param name="max_dist_relations" type="integer" value="3" label="maximum distance relations" help="-D"/>
+    </inputs>
+    <outputs>
+        <data name="data_svector" format="zip" from_work_dir="SVECTOR/data.svector" label="data_svector"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="data_fasta" value="data.fasta"/>
+            <param name="gspan_file" value="1.group.gspan.bz2" ftype="searchgui_archive"/>
+            <param name="max_rad" value="3"/>
+            <param name="max_dist_relations" value="3"/>
+            <output name="data_svector" file="SVECTOR/data.svector" ftype="zip" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
 
 **What it does**
 
@@ -45,22 +49,22 @@
 
 **Parameters**
 
-+	**-R** <max radius> (default: 1)
-+	**-D** <max distance relations> (default: 4)
++    **-R** <max radius> (default: 1)
++    **-D** <max distance relations> (default: 4)
 
 
     ]]>
-	</help>
-	<citations>
-		<citation type="doi">10.1093/bioinformatics/bts224</citation>
-		<citation type="bibtex">@inproceedings{costa2010fast,
-      title={Fast neighborhood subgraph pairwise distance kernel},
-      author={Costa, Fabrizio and De Grave, Kurt},
-      booktitle={Proceedings of the 26th International Conference on Machine Learning},
-      pages={255--262},
-      year={2010},
-      organization={Omnipress}
-    }
-	</citation>
-	</citations>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts224</citation>
+        <citation type="bibtex">@inproceedings{costa2010fast,
+          title={Fast neighborhood subgraph pairwise distance kernel},
+          author={Costa, Fabrizio and De Grave, Kurt},
+          booktitle={Proceedings of the 26th International Conference on Machine Learning},
+          pages={255--262},
+          year={2010},
+          organization={Omnipress}
+        }
+        </citation>
+    </citations>
 </tool>