Mercurial > repos > enios > nc_rna

changeset 12:b612b035a493 draft

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Deleted selected files
author enios
date Sat, 22 May 2021 07:29:26 +0000
parents 606b4c26156b
children da21e15c8365
files cbind.xml csv2json.xml interactions.xml rankprod2.xml
diffstat 4 files changed, 0 insertions(+), 104 deletions(-) [+]
line wrap: on
line diff
--- a/cbind.xml	Sun May 16 12:16:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<tool id="cbind" name="Cbind" >
-    <description>cbind horizontally</description>
-    <requirements>
-        <container type="docker">bianca7/lncrna:cbind</container>
-    </requirements>
-    <command><![CDATA[ python /var/lib/pandas/rbind.py 
-        #for $q in $queries
-	'${q.input2}' 
-	#end for
-	&& mv mergedArray.txt $out_file1
-	    ]]></command>
-    <inputs>
-        <!--param name="input1" type="data" label="Concatenate Dataset"/-->
-        <repeat name="queries" title="Dataset">
-            <param name="input2" type="data" label="Select" />
-        </repeat>
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="input" metadata_source="input1"/>
-    </outputs>
-</tool>
-
--- a/csv2json.xml	Sun May 16 12:16:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<tool id="csv2json" name="csv2json" >
-<requirements>
-	<container type="docker">bianca7/lncrna:csv2json</container>
-</requirements>
-<description>CSV to JSON for Cytoscape.js visualization</description>
-<command><![CDATA[ python /code/csv2json.py --file "$input" && cp *.json "$output"
-]]></command>
-<inputs>
-	<param name="input" type="data" label="CSV input (rnaInteractions output)"/>
-</inputs>
-<outputs>
-	<data name="output" format="json"/>
-</outputs>
-</tool>
-
--- a/interactions.xml	Sun May 16 12:16:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,21 +0,0 @@
-<tool id="interactions" name="rnaInteractions" >
- <requirements>
-     <container type="docker">bianca7/lncrna:interactions</container>
- </requirements>
- <description>RNA-RNA interactions from RISE and NPINTER databases</description>
- <stdio>
-   <exit_code range="1:" level="fatal" />
- </stdio>
- <command><![CDATA[ Rscript /code/interactions.R $RNAs_file && cp bim_triplnetwork.tsv "$output1" && cp cs_triplnetwork.tsv "$output2" && cp bim_mRNAtarget.tsv "$output3" && cp cs_mRNAtarget.tsv "$output4" && cp not_found_interactions.tsv "$output5"
-  ]]></command>
-  <inputs>
-   <param format="tabular,txt" name="RNAs_file" type="data" label="differentially expressed RNA molecules (RankProd output in our lncRNA workflow)" />
- </inputs>
- <outputs>
-    <data format="tabular" name="output1" label="Interactions' triplets (biotranslator input)"/>
-    <data format="tabular" name="output2" label="Interactions' triplets (cytoscape input)"/>
-    <data format="tabular" name="output3" label="mRNA reverse expressions (biotranslator input)"/>
-    <data format="tabular" name="output4" label="mRNA reverse expressions (cytoscape input)"/>
-    <data format="tabular" name="output5" label="RNAs not found in interactions' DBs (RiBlast input)"/>
- </outputs>
-</tool>
--- a/rankprod2.xml	Sun May 16 12:16:03 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-<tool id="rankprodthree" name="RankProd" >
- <requirements>
-     <container type="docker">bianca7/lncrna:rankprod</container>
- </requirements>
- <description>Differential expression with RankProd</description>
- <stdio>
-   <exit_code range="1:" level="fatal" />
- </stdio>
- <command><![CDATA[
-       #if $choose.genes=='T'
-      Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.numgenes
-     #end if
-     #if $choose.genes=='F'
-      Rscript /logrankprod.R "c($whichcols)" $file1 "c($whichrows)" $sc $file2 $file3 $norm $base $log $choose.genes $choose.method $choose.cutoff
-     #end if
-  ]]></command>
-  <inputs>
-   <param format="tabular, txt" name="file1" type="data" label="input matrix" />
-   <param name="whichcols" type="text" label="Comma separated fields for columns, like 1,2,3,4" />
-   <param name="sc" type="integer" value="1" label="Choose col class" />
-   <param format="tabular, txt" name="file2" type="data" label="input samples matrix" />
-   <param name="whichrows" type="text" label="Comma separated fields for rows" />
-   <param name="norm" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are counts normalized?" />
-   <param name="base" type="select" label="Choose log base" >
-     <option value="2">2</option>
-     <option value="10">10</option>
-   </param>
-   <param name="log" type="boolean" truevalue="T" falsevalue="F" selected="FALSE" label="Are they logarithmically transformed?" />
-   <conditional name="choose" >
-     <param name="genes" type="boolean" truevalue="T" falsevalue="F" checked="no" label="Select specific genes or choose method" />
-     <when value="T">
-       <param name="numgenes" type="integer" value="10" label="How many genes" />
-     </when>
-     <when value="F">
-       <param name="method" type="select" label="Select method" >
-        <option value="pfp">pfp</option>
-        <option value="pval">pval</option>
-       </param>
-       <param name="cutoff" type="float" value="0.05" label="Choose cutoff" />
-     </when>
-   </conditional>
- </inputs>
- <outputs>
-    <data format="txt" name="file3" label="Differentially expressed molecules"/>
- </outputs>
-</tool>