| Previous changeset 0:e13ec2c3fabe (2016-07-04) Next changeset 2:3a9914b37f2f (2016-07-04) |
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Commit message:
planemo upload commit 1c73dd5ed7b5b8595963e0e1b6f8427978d8d5f5-dirty |
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modified:
ProbMetab.xml |
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added:
macros.xml |
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| diff -r e13ec2c3fabe -r c4bd0c40eb3b ProbMetab.xml --- a/ProbMetab.xml Mon Jul 04 04:29:25 2016 -0400 +++ b/ProbMetab.xml Mon Jul 04 09:51:51 2016 -0400 |
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| @@ -2,18 +2,15 @@ <description>Wrapper function for ProbMetab R package.</description> - <requirements> - <requirement type="package" version="0.4_1">r-snow</requirement> - <requirement type="package" version="1.0">r-probmetab</requirement> - <requirement type="package" version="1.1_4">r-batch</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> + <expand macro="requirements"/> + <expand macro="stdio"/> <command> - LANG=C Rscript $__tool_directory__/probmetab.r + @COMMAND_CAMERA_SCRIPT@ #if $acquisition_options.mode == "one": mode_acquisition $acquisition_options.mode xa $acquisition_options.xa ##if $acquisition_options.xsetnofill_options.option == "show": @@ -39,9 +36,7 @@ allowMiss $allowMiss html $html kegg_db $kegg_db ppm_tol $ppm_tol opt $opt corths $corths corprob $corprob pcorprob $pcorprob prob $prob - #if $zip_file: - zipfile $zip_file - #end if + @COMMAND_ZIPFILE_LOAD@ </command> @@ -161,9 +156,7 @@ --> - <!-- To pass planemo test --> - <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> - + <expand macro="zipfile_load"/> </inputs> <outputs> @@ -197,7 +190,8 @@ <test> <param name="acquisition_options|mode" value="one" /> <param name="acquisition_options|xa" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> - <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> + <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> <output name="log"> <assert_contents> <has_text text="ko15 ko16 wt15 wt16" /> @@ -213,25 +207,7 @@ <help> -.. class:: infomark - -**Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br - - | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics.. - | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/ - -.. class:: infomark - -**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - -.. class:: infomark - -**Contributors** Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr - ---------------------------------------------------- - +@HELP_AUTHORS@ ========= ProbMetab @@ -419,10 +395,8 @@ </help> - <citations> - <citation type="doi">10.1093/bioinformatics/btu019</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + + <expand macro="citation" /> </tool> |
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| diff -r e13ec2c3fabe -r c4bd0c40eb3b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 04 09:51:51 2016 -0400 |
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| @@ -0,0 +1,69 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.4_1">r-snow</requirement> + <requirement type="package" version="1.0">r-probmetab</requirement> + <requirement type="package" version="1.1_4">r-batch</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + </xml> + + <token name="@COMMAND_CAMERA_SCRIPT@"> + LANG=C Rscript $__tool_directory__/probmetab.r + </token> + + <!-- zipfile load for planemo test --> + <token name="@COMMAND_ZIPFILE_LOAD@"> + #if $zipfile_load_conditional.zip_file: + zipfile $zipfile_load_conditional.zip_file + #end if + </token> + <xml name="zipfile_load"> + <conditional name="zipfile_load_conditional"> + <param name="zipfile_load_select" type="select" label="Resubmit your zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." > + <option value="no" >no need</option> + <option value="yes" selected="peakgroups">yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" /> + </when> + </conditional> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Ricardo R. Silva et al. (2013) rsilvabioinfo@usp.br + + | If you use this tool, please cite: Silva RR and al.(2010). ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics.. + | For details about this tool, please go to http://labpib.fmrp.usp.br/methods/probmetab/ + +.. class:: infomark + +**Galaxy integration** Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABIMS TEAM, Station biologique de Roscoff. + + | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. + +.. class:: infomark + +**Contributors** Ricardo R. Silva rsilvabioinfo@usp.br, Yann Guitton yann.guitton@univ-nantes.fr and Jean-François Martin jean-francois.martin@toulouse.inra.fr + +--------------------------------------------------- + + </token> + + + <xml name="citation"> + <citations> + <citation type="doi">10.1093/bioinformatics/btu019</citation> + <citation type="doi">10.1093/bioinformatics/btu813</citation> + </citations> + </xml> +</macros> |