Mercurial > repos > devteam > picard
diff picard_MeanQualityByCycle.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_MeanQualityByCycle.xml Sun Nov 27 15:11:36 2016 -0500 +++ b/picard_MeanQualityByCycle.xml Tue Dec 06 10:04:26 2016 -0500 @@ -9,30 +9,30 @@ <command detect_errors="exit_code"><![CDATA[ @java_options@ ##set up input files - + @symlink_element_identifier@ #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( $reference_source.ref_file.fields.path ) #end if - + picard MeanQualityByCycle - INPUT="${inputFile}" + INPUT='$inputFile.element_identifier' OUTPUT="${outFile}" CHART_OUTPUT="${pdfFile}" REFERENCE_SEQUENCE="${reference_fasta_filename}" ALIGNED_READS_ONLY="${aligned_reads_only}" PF_READS_ONLY="${pf_reads_only}" - + ASSUME_SORTED="${assume_sorted}" - + VALIDATION_STRINGENCY="${validation_stringency}" QUIET=true VERBOSITY=ERROR - + ]]></command> <inputs> <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> @@ -55,16 +55,16 @@ <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> <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" label="${tool.name} on ${on_string}: Summary data"/> <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> </outputs> - + <tests> <test> <param name="assume_sorted" value="true" /> @@ -74,31 +74,31 @@ <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/> - </test> + </test> </tests> - - + + <help> .. class:: infomark **Purpose** -Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. +Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. @dataset_collections@ @description@ - ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: - false. Possible values: {true, false} + ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: + false. 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} ASSUME_SORTED=Boolean - AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True @more_info@