Mercurial > repos > biancakrieger > nc_rna_enios

changeset 5:d72d2ed9efac draft default tip

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Deleted selected files
author biancakrieger
date Wed, 21 Apr 2021 10:35:29 +0000
parents 1831c7f4c173
children
files ezlncpred.xml interactions.xml lncadeep.xml rankprod2.xml tcga_heatmap.xml
diffstat 5 files changed, 0 insertions(+), 141 deletions(-) [+]
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--- a/ezlncpred.xml	Wed Apr 21 10:09:28 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<tool id="ezlncpred" name="ezLncPred" >
-    <description>"ezLncPred"</description>
-    <requirements>
-        <container type="docker">eniosorg/bim:ezlncpred</container>
-    </requirements>
-    <command><![CDATA[ezLncPred -i $fasta_file -o out $model
-      #if $model =="CPAT"
-        -p Human
-      #end if
-      #if $model =="CPPred"
-        -p Human
-      #end if
-      #if $model =="longdist"
-        -z 200 -p Human
-      #end if
-      && mv out $out
-   ]]></command>
-   <inputs>
-     <param type="data" name="fasta_file" format="fasta" />
-     <param type="select" name="model">
-       <!--option value="CNCI">CNCI</option>
-       <option value="CPC2">CPC2</option-->
-       <option value="CPAT">CPAT</option>
-       <option value="lgc">lgc</option>
-       <option value="CPPred">CPPred</option>
-       <!--option value="GFStack">GFStack</option-->
-       <option value="longdist">longdist</option>
-       <!--option value="PLEK">PLEK</option>
-       <option value="LncADeep">LncDeep</option-->
-     </param>
-  </inputs>
-  <outputs>
-    <data name="out" format="txt" from_work_directory="out"/>
-  </outputs>
-</tool>
--- a/interactions.xml	Wed Apr 21 10:09:28 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/lncadeep.xml	Wed Apr 21 10:09:28 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<tool id="lncadeep" name="LncADeep" >
-    <description>"LncADeep"</description>
-    <requirements>
-        <container type="docker">bianca7/lncadeep</container>
-    </requirements>
-    <command><![CDATA[python /usr/local/lib/python2.7/site-packages/LncADeep/LncADeep.py -MODE anno
-      -o test
-      -l $RNA_FILE
-      -p $PROTEIN_FILE
-      -a 1
-      && tar -cvf results.tar test_LncADeep_anno_results && mv results.tar $results
-    ]]></command>
-    <inputs>
-        <param type="data" name="RNA_FILE" format="fasta" label="RNA  sequences in FASTA format" />
-        <param type="data" name="PROTEIN_FILE" format="fasta" label="protein sequences in FASTA format" />
-    </inputs>
-    <outputs>
-        <data name="results" format="tar" />
-    </outputs>
-</tool>
--- a/rankprod2.xml	Wed Apr 21 10:09:28 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>
--- a/tcga_heatmap.xml	Wed Apr 21 10:09:28 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<tool id="tcga_heatmap" name="TCGA_HEATMAP" >
- <requirements>
-     <container type="docker">bianca7/lncrna:tcga</container>
- </requirements>
- <description>Test your signature on TCGA data</description>
- <stdio>
-   <exit_code range="1:" level="fatal" />
- </stdio>
- <command><![CDATA[ Rscript /Heatmap1.R -g "$signature" -c "$cancer_type" -R "/$output1" -o "/$output2"
-  ]]></command>
-  <inputs>
-   <param format="tabular,txt" name="signature" type="data" label="gene signature" />
-   <param name="cancer_type" type="text" label="TCGA-cancer project" />
- </inputs>
- <outputs>
-    <data format="pdf" name="output1" label="Heatmap"/>
-    <data format="html" name="output2" label="Heatmap"/>
- </outputs>
-</tool>