| Next changeset 1:ae1ad90ca587 (2018-06-05) |
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Commit message:
planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272-dirty |
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added:
ExtractFromSDFiles.xml tool_dependencies.xml |
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| diff -r 000000000000 -r e3086f60b0e4 ExtractFromSDFiles.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ExtractFromSDFiles.xml Fri Jun 01 04:57:02 2018 -0400 |
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| @@ -0,0 +1,43 @@ +<tool id="ExtractFromSDFiles" name="ExtractFromSDFiles" version="1.0"> +<description>extract data from file according to field name and Ids </description> +<requirements> + <requirement type="package" version="9.0">mayachemtools</requirement> +</requirements> +<stdio> + <exit_code range="1:" /> +</stdio> + +<command> <![CDATA[ + +#if '.sdf' in $inputsdf.name + +/bin/mkdir -p $inputsdf.extra_files_path; +ln -sf $inputsdf $inputsdf.extra_files_path/molecules.sdf; + +ExtractFromSDFiles.pl -o -m datafieldbylist -d $Identifier,`cat ${indexnumbers}` -r $outputsdf.name $inputsdf.extra_files_path/molecules.sdf > $logs; + +/bin/rm -rf $inputsdf.extra_files_path; +cp $outputsdf.name $outputsdf; + +#end if + +]]> </command> + <inputs> + <param name="inputsdf" type="data" format="sdf" label="Original SDF File " help="sdf file from which selected ids of molecules need to be extracted." /> + <param name="Identifier" type="text" label="Field name" help="Give field name of molecules on which compound need to be extracted Ex. MolID,PUBCHEM_COMPOUND_ID,CID etc." /> + <param name="indexnumbers" type="data" format="txt" label="Id file which need to be extracted from dataset" help="select file of ids ie. result file obtained from the tool 'Extract IDs From Prediction Result'" /> + </inputs> + <outputs> + <data name="outputsdf" format="sdf" label="extracted_cpds_from_${inputsdf.name}" /> + <data name="logs" format="txt" label="logfile" /> + </outputs> + <tests> + <test> + <param name="inputsdf" value="Pred_set.sdf" /> + <param name="Identifier" value="MOLECULE_NAME" /> + <param name="indexnumbers" value="extracted_ids.txt" /> + <output name="outputsdf" file="extracted_cpds.sdf" compare="sim_size" delta="8000000" /> + <output name="logs" file="ext_log.txt" compare="sim_size" delta="800000" /> + </test> + </tests> +</tool> |
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| diff -r 000000000000 -r e3086f60b0e4 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 01 04:57:02 2018 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mayachemtools" version="9.0"> + <repository changeset_revision="621b85a1b927" name="package_mayachemtools_9_0" owner="anmoljh" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu/" /> + </package> +</tool_dependency> |