Mercurial > repos > devteam > picard
diff picard_CollectBaseDistributionByCycle.xml @ 8:e417b1d6288d draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author | devteam |
---|---|
date | Tue, 06 Dec 2016 10:04:26 -0500 |
parents | 08f69add4d06 |
children | 41b8d087a2d2 |
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--- a/picard_CollectBaseDistributionByCycle.xml Sun Nov 27 15:11:36 2016 -0500 +++ b/picard_CollectBaseDistributionByCycle.xml Tue Dec 06 10:04:26 2016 -0500 @@ -8,30 +8,31 @@ </expand> <command detect_errors="exit_code"><![CDATA[ @java_options@ + @symlink_element_identifier@ ##set up input files #set $reference_fasta_filename = "localref.fa" - + #if str( $reference_source.reference_source_selector ) == "history": ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if - + picard CollectBaseDistributionByCycle - INPUT="${inputFile}" + INPUT='$inputFile.element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" ALIGNED_READS_ONLY="${aligned_reads_only}" PF_READS_ONLY="${pf_reads_only}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ASSUME_SORTED="${assume_sorted}" - + VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></command> <inputs> <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> @@ -51,19 +52,19 @@ <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> </when> </conditional> - <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/> - <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> - <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> - + <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/> + <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + <expand macro="VS" /> - + </inputs> - + <outputs> <data format="tabular" name="outFile"/> <data format="pdf" name="pdfFile"/> </outputs> - + <tests> <test> <param name="aligned_reads_only" value="true" /> @@ -75,8 +76,8 @@ <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/> </test> </tests> - - + + <help> .. class:: infomark @@ -89,19 +90,19 @@ @description@ - ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: - false. This option can be set to 'null' to clear the default value. Possible values: - {true, false} + ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: + false. This option can be set to 'null' to clear the default value. Possible values: + {true, false} - PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. - This option can be set to 'null' to clear the default value. Possible values: {true, - false} + PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. + This option can be set to 'null' to clear the default value. Possible values: {true, + false} REFERENCE_SEQUENCE=File - R=File Reference sequence fasta Default value: null. + R=File Reference sequence fasta Default value: null. ASSUME_SORTED=Boolean - AS=Boolean If true (default), then the sort order in the header file will be ignored. Default + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default @more_info@