Mercurial > repos > iuc > dexseq
changeset 3:a26a82bed63f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2a2d5182035489c6334c31a3be755365ef22fe96
| author | iuc |
|---|---|
| date | Fri, 25 Sep 2015 16:26:39 -0400 |
| parents | b19cb9385f28 |
| children | 7069d55968fb |
| files | dexseq.xml dexseq_count.xml tool_dependencies.xml |
| diffstat | 3 files changed, 35 insertions(+), 33 deletions(-) [+] |
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--- a/dexseq.xml Fri Sep 25 15:57:00 2015 -0400 +++ b/dexseq.xml Fri Sep 25 16:26:39 2015 -0400 @@ -4,6 +4,20 @@ <requirement type="package" version="1.14">dexseq</requirement> </requirements> <code file="dexseq_helper.py" /> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Input-Error 01" + source="both" + level="fatal" + description="Error in your input parameters: Make sure you only apply factors to selected samples." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> <command> <![CDATA[ mkdir ./html_out && @@ -38,22 +52,8 @@ && ]]> </command> - <stdio> - <regex match="Execution halted" - source="both" - level="fatal" - description="Execution halted." /> - <regex match="Input-Error 01" - source="both" - level="fatal" - description="Error in your input parameters: Make sure you only apply factors to selected samples." /> - <regex match="Error in" - source="both" - level="fatal" - description="An undefined error occured, please check your intput carefully and contact your administrator." /> - </stdio> <inputs> - <param name="gtf" type="data" label="GTF file created from DEXSeq-Count tool"/> + <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/> <repeat name="rep_factorName" title="Factor" min="1"> <param name="factorName" type="text" value="FactorName" label="Specify a factor name" help="Only letters, numbers and underscores will be retained in this field"> @@ -68,7 +68,7 @@ <valid initial="string.letters,string.digits"><add value="_" /></valid> </sanitizer> </param> - <param name="countsFile" type="data" multiple="true" label="Counts file"/> + <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file"/> </repeat> </repeat> <param name="report" type="boolean" truevalue="" falsevalue="" checked="true" @@ -76,15 +76,12 @@ help="output an additional html file" /> <param name="fdr_cutoff" type="float" min="0" max="1" value="0.05" label="All the genes under this FDR threshold will be shown in the html report."/> </inputs> - <outputs> <data format="tabular" name="dexseq_out" label="DEXSeq result file on ${on_string}"/> <data format="html" name="htmlreport" label="DEXSeq report on ${on_string}"> <filter>report == True</filter> </data> </outputs> - - <code file="dexseq_helper.py" /> <tests> <test> <param name="gtf" value="dexseq.gtf" ftype="bed"/>
--- a/dexseq_count.xml Fri Sep 25 15:57:00 2015 -0400 +++ b/dexseq_count.xml Fri Sep 25 16:26:39 2015 -0400 @@ -1,11 +1,18 @@ <tool id="dexseq_count" name="DEXSeq-Count" version="1.0"> <description>Prepare and count exon abundancies from RNA-seq data</description> <requirements> - <requirement type="package" version="3.1.0">R</requirement> - <requirement type="package" version="1.14.2">dexseq</requirement> + <requirement type="package" version="1.14">dexseq</requirement> <requirement type="package" version="0.6.1">htseq</requirement> - <requirement type="package" version="0.7.6">pysam</requirement> + <requirement type="package" version="0.7.7">pysam</requirement> </requirements> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> <command> <![CDATA[ #if $mode.mode_select == "prepare": @@ -26,14 +33,6 @@ #end if ]]> </command> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> <inputs> <conditional name="mode"> <param name="mode_select" type="select" label="Mode of operation"> @@ -66,10 +65,10 @@ <outputs> <data format="tabular" name="counts_file" label="DEXSeq count reads on ${on_string}"> - <filter>(mode['mode_select'] == 'count')</filter> + <filter>mode['mode_select'] == 'count'</filter> </data> - <data format="gff" name="flattened_gtf_out" label="DEXSeq prepare annotation ${on_string}"> - <filter>(mode['mode_select'] == 'prepare')</filter> + <data format="gtf" name="flattened_gtf_out" label="DEXSeq prepare annotation on ${on_string}"> + <filter>mode['mode_select'] == 'prepare'</filter> </data> </outputs>
--- a/tool_dependencies.xml Fri Sep 25 15:57:00 2015 -0400 +++ b/tool_dependencies.xml Fri Sep 25 16:26:39 2015 -0400 @@ -1,5 +1,11 @@ <?xml version="1.0"?> <tool_dependency> + <package name="pysam" version="0.7.7"> + <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="htseq" version="0.6.1"> + <repository changeset_revision="025da27a2bb2" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> <package name="dexseq" version="1.14"> <repository changeset_revision="cb7ad0ece9e8" name="package_dexseq_1_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package>