Mercurial > repos > rnateam > graphclust_nspdk

changeset 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
files NSPDK_candidateClusters.xml NSPDK_sparseVect.xml
diffstat 2 files changed, 167 insertions(+), 153 deletions(-) [+]
line wrap: on
line diff
--- a/NSPDK_candidateClusters.xml	Mon Feb 27 12:03:12 2017 -0500
+++ b/NSPDK_candidateClusters.xml	Mon Mar 13 18:05:04 2017 -0400
@@ -1,113 +1,123 @@
 <tool id="NSPDK_candidateClust" name="NSPDK_candidateClusters" version="9.2">
-	<requirements>
-		<requirement type="package" version="0.1.8">graphclust-wrappers</requirement>
-		<requirement type="package" version="0.5">perl-array-utils</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="0.5">perl-array-utils</requirement>
+    <requirement type="package" version="9.2">nspdk</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command>
+       <![CDATA[
 
-        mkdir -p SVECTOR &&
-
-        cp $data_svector SVECTOR/data.svector &&
-
-        'NSPDK_candidateClusters.pl'  '$data_fasta' '$data_names' $noCache $ensf $oc $usn $knn $nhf $nspdk_nhf_max $nspdk_nhf_step $GLOBAL_num_clusters $max_rad $max_dist_relations
+        mkdir ./SVECTOR &&
 
-        #if  $iteration_num.iteration_num_selector:
-          $iteration_num.CI
-          '$blacklist'
-          '$final_partition_soft'
-          '$fast_cluster_last_round'
-          $iteration_num.GLOBAL_hit_blacklist_overlap
+        #for $ins in $data_svector:
+            ln -f -s  '$ins' ./SVECTOR/ &&
+        #end for
 
-        #else:
-          1
-
-        #end if
+        NSPDK_candidateClusters.pl
+            '$data_fasta'
+            '$data_names'
+            $noCache
+            $ensf
+            $oc
+            $usn
+            $knn
+            $nhf
+            $nspdk_nhf_max
+            $nspdk_nhf_step
+            $GLOBAL_num_clusters
+            $max_rad
+            $max_dist_relations
 
-]]>
-	</command>
-	<inputs>
-		<param type="data" name="data_svector" format="zip"  />
-		<param type="data" name="data_fasta" format="fasta" />
-		<param type="data" name="data_names" format="txt" />
-		<conditional name="iteration_num">
-			<param name="iteration_num_selector" type="boolean"  checked="no" label="Multiple iterations"  help="for single iteration- NO, for multiple-YES"/>
-			<when value="true">
-				<param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
-				<param type="data" name="blacklist" format="txt" />
-				<param type="data" name="final_partition_soft" format="txt" />
-				<param type="data" name="fast_cluster_last_round" format="txt" />
-				<param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />
-			</when>
-			<when value="false" >
-				<param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>
-			</when>
-		</conditional>
-		<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"/>
-		<param name="noCache" truevalue="-no-cache" falsevalue="" checked="True" type="boolean"
+        #if $iteration_num.iteration_num_selector:
+            $iteration_num.CI
+            '$blacklist'
+            '$final_partition_soft'
+            '$fast_cluster_last_round'
+            $iteration_num.GLOBAL_hit_blacklist_overlap
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param type="data" name="data_svector"  multiple="True"/>
+        <param type="data" name="data_fasta" format="fasta" />
+        <param type="data" name="data_names" format="txt" />
+        <conditional name="iteration_num">
+        <param name="iteration_num_selector" type="boolean"  checked="no" label="Multiple iterations"  help="for single iteration- NO, for multiple-YES"/>
+        <when value="true">
+                <param name="CI" type="integer" value="2" size="5" label="Number of current iteration "/>
+                <param type="data" name="blacklist" format="txt" />
+                <param type="data" name="final_partition_soft" format="txt" />
+                <param type="data" name="fast_cluster_last_round" format="txt" />
+                <param name="GLOBAL_hit_blacklist_overlap" type="float" value="0.2" size="5" label="Blacklist hit overlap" />
+            </when>
+            <when value="false" >
+                <param name="CI" type="hidden" value="1" size="5" label="Number of current iteration "></param>
+            </when>
+        </conditional>
+        <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"/>
+        <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="ensf" type="integer" value="5" size="5" label="eccess neighbour size factor" help="-ensf"/>
+        <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"
+        <param name="oc" truevalue="-oc" falsevalue="" checked="True" type="boolean"
                 label=" flag to output clusters (-oc)" help="by default true"/>
-		<param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/>
-		<param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>
-		<param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />
-		<param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/>
-		<param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />
-	</inputs>
-	<outputs>
-		<data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1"  >
-			<filter> iteration_num['iteration_num_selector'] is False</filter>
-		</data>
-		<data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >
-			<filter> iteration_num['iteration_num_selector'] is False </filter>
-		</data>
-		<data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >
-			<filter> iteration_num['iteration_num_selector'] is False </filter>
-		</data>
-		<data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI"  >
-			<filter> iteration_num['iteration_num_selector'] is True</filter>
-		</data>
-		<data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >
-			<filter> iteration_num['iteration_num_selector'] is True</filter>
-		</data>
-		<data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >
-			<filter> iteration_num['iteration_num_selector'] is True</filter>
-		</data>
-	</outputs>
-	<tests>
-		<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"  />
-			<conditional name="iteration_num">
-				<param name="iteration_num_selector" value="false"/>
-			</conditional>
-			<param name="noCache" value="-no-cache"/>
-			<param name="ensf" value="5"/>
-			<param name="oc" value="-oc"/>
-			<param name="max_rad" value="3"/>
-			<param name="max_dist_relations" value="3"/>
-			<param name="usn" value="-usn"/>
-			<param name="knn" value="20"/>
-			<param name="nhf" value="500"/>
-			<param name="nspdk_nhf_max" value="1000"/>
-			<param name="nspdk_nhf_step" value="25"/>
-			<param name="GLOBAL_num_clusters" value="100"/>
-			<output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />
-			<output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />
-			<output name="black_list" file="SVECTOR/data.svector.blacklist.1" />
-		</test>
-	</tests>
-	<help>
-		<![CDATA[
+        <param name="knn" type="integer" value="20" size="5" label="Number of nearest neighbors" help="-knn num"/>
+        <param name="nhf" type="integer" value="500" size="5" label="Number of hash functions " help="-nhf num"/>
+        <param name="nspdk_nhf_max" type="integer" value="1000" size="5" label="Maximal number of hash functions " />
+        <param name="nspdk_nhf_step" type="integer" value="25" size="5" label="Size of step for increasing hash functions " help="The number of hash functions is increased by this value after each iteration."/>
+        <param name="GLOBAL_num_clusters" type="integer" value="100" size="5" label="Maxinum number of clusters " />
+    </inputs>
+    <outputs>
+        <data name="fast_cluster" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster" label="fast_cluster.1"  >
+            <filter> iteration_num['iteration_num_selector'] is False</filter>
+        </data>
+        <data name="fast_cluster_sim" format="txt" from_work_dir="SVECTOR/data.svector.1.fast_cluster_sim" label="fast_cluster_sim.1" >
+            <filter> iteration_num['iteration_num_selector'] is False </filter>
+        </data>
+        <data name="black_list" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.1" label="blacklist.1" >
+            <filter> iteration_num['iteration_num_selector'] is False </filter>
+        </data>
+        <data name="fast_cluster_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster" label="fast_cluster.$iteration_num.CI"  >
+            <filter> iteration_num['iteration_num_selector'] is True</filter>
+        </data>
+        <data name="fast_cluster_sim_m" format="txt" from_work_dir="SVECTOR/data.svector.*.fast_cluster_sim" label="fast_cluster_sim.$iteration_num.CI" >
+            <filter> iteration_num['iteration_num_selector'] is True</filter>
+        </data>
+        <data name="black_list_m" format="txt" from_work_dir="SVECTOR/data.svector.blacklist.*" label="blacklist.$iteration_num.CI" >
+            <filter> iteration_num['iteration_num_selector'] is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <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"  />
+            <conditional name="iteration_num">
+                <param name="iteration_num_selector" value="false"/>
+            </conditional>
+            <param name="noCache" value="-no-cache"/>
+            <param name="ensf" value="5"/>
+            <param name="oc" value="-oc"/>
+            <param name="max_rad" value="3"/>
+            <param name="max_dist_relations" value="3"/>
+            <param name="usn" value="-usn"/>
+            <param name="knn" value="20"/>
+            <param name="nhf" value="500"/>
+            <param name="nspdk_nhf_max" value="1000"/>
+            <param name="nspdk_nhf_step" value="25"/>
+            <param name="GLOBAL_num_clusters" value="100"/>
+            <output name="fast_cluster" file="SVECTOR/data.svector.1.fast_cluster" />
+            <output name="fast_cluster_sim" file="SVECTOR/data.svector.1.fast_cluster_sim" />
+            <output name="black_list" file="SVECTOR/data.svector.blacklist.1" />
+        </test>
+    </tests>
+    <help>
+        <![CDATA[
 
 **What it does**
 
@@ -133,10 +143,10 @@
 
 
     ]]>
-	</help>
-	<citations>
-		<citation type="doi">10.1093/bioinformatics/bts224</citation>
-		<citation type="bibtex">@inproceedings{costa2010fast,
+    </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},
@@ -145,5 +155,5 @@
         organization={Omnipress}
       }
       </citation>
-	</citations>
+    </citations>
 </tool>
--- 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>