Mercurial > repos > rnateam > graphclust_nspdk

changeset 5:9b5fb987a484 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/NSPDK commit b'7e5cd452018ae9507c2d1cd13dd688a747550393\n'
author rnateam
date Fri, 17 Mar 2017 08:28:51 -0400
parents 0625db6b6e45
children 2aaf391798a3
files NSPDK_candidateClusters.xml NSPDK_sparseVect.xml test-data/1.group.gspan test-data/data.svector.1
diffstat 4 files changed, 7 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/NSPDK_candidateClusters.xml	Mon Mar 13 18:05:04 2017 -0400
+++ b/NSPDK_candidateClusters.xml	Fri Mar 17 08:28:51 2017 -0400
@@ -1,8 +1,8 @@
 <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">
     <requirements>
-        <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
+        <requirement type="package" version="0.1.11">graphclust-wrappers</requirement>
         <requirement type="package" version="0.5">perl-array-utils</requirement>
-    <requirement type="package" version="9.2">nspdk</requirement>
+        <requirement type="package" version="9.2">nspdk</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -13,7 +13,7 @@
         mkdir ./SVECTOR &&
 
         #for $ins in $data_svector:
-            ln -f -s  '$ins' ./SVECTOR/ &&
+            ln -f -s  '$ins' ./SVECTOR/$ins.element_identifier &&
         #end for
 
         NSPDK_candidateClusters.pl
@@ -62,7 +62,7 @@
         <param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
                 label="Deactivate caching of kernel value computation  (-no-cache)" help="to minimize memory usage"/>
         <param name="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/>
-        <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"    
+        <param name="usn" truevalue="-usn" falsevalue="" checked="True" type="boolean"
                 label="Use shared neighbourhood to weight center density (-usn)" help="by default true"/>
         <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
                 label=" flag to output clusters (-oc)" help="by default true"/>
@@ -96,7 +96,7 @@
         <test>
             <param name="data_fasta" value="data.fasta"/>
             <param name="data_names" value="data.names"/>
-            <param name="data_svector" value="data.svector.1" ftype="zip"  />
+            <param name="data_svector" value="1.group.gspan"   />
             <conditional name="iteration_num">
                 <param name="iteration_num_selector" value="false"/>
             </conditional>
--- a/NSPDK_sparseVect.xml	Mon Mar 13 18:05:04 2017 -0400
+++ b/NSPDK_sparseVect.xml	Fri Mar 17 08:28:51 2017 -0400
@@ -1,6 +1,6 @@
 <tool id="nspdk_sparse" name="NSPDK_sparseVect" version="9.2">
     <requirements>
-        <requirement type="package" version="0.1.10">graphclust-wrappers</requirement>
+        <requirement type="package" version="0.1.11">graphclust-wrappers</requirement>
         <requirement type="package" version="9.2">nspdk</requirement>
     </requirements>
     <stdio>
@@ -9,7 +9,6 @@
     <command>
         <![CDATA[
 
-
         NSPDK_sparseVect.pl
             '$data_fasta'
             '$gspan_file'
@@ -19,7 +18,7 @@
 ]]>
     </command>
     <inputs>
-        <param type="data" name="gspan_file" />
+        <param type="data" name="gspan_file" format="txt" label="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"/>
Binary file test-data/1.group.gspan has changed
Binary file test-data/data.svector.1 has changed