Mercurial > repos > bgruening > hicup_filter
diff hicup_filter.xml @ 4:a7bbbf32da62 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author | bgruening |
---|---|
date | Fri, 25 May 2018 17:49:27 -0400 |
parents | b16228ec1540 |
children | daf29b40670f |
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--- a/hicup_filter.xml Thu Nov 09 11:16:04 2017 -0500 +++ b/hicup_filter.xml Fri May 25 17:49:27 2018 -0400 @@ -1,59 +1,64 @@ -<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0"> - <description>classifies read pairs, identifying valid Hi-C di-tags.</description> +<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" profile="18.01"> + <description>classifies read pairs, identifying valid Hi-C di-tags</description> <macros> <import>hicup_macros.xml</import> </macros> - <expand macro="requirements_hicup" /> - <expand macro="stdio" /> - <command><![CDATA[ - hicup_filter --digest '$digest' + <expand macro="requirements_hicup"/> + <command detect_errors="exit_code"><![CDATA[ + #for $i, $file in enumerate($inputFiles): + #if $file.ext != 'sam': + ln -s '$file' ./${i}.bam && + #end if + #end for + hicup_filter --zip --digest '$digest' #if $advanced_options.longest: --longest '$advanced_options.longest' #end if #if $advanced_options.shortest: --shortest '$advanced_options.shortest' #end if - #for $file in $inputFiles: - $file + #for $i, $file in enumerate($inputFiles): + #if $file.ext != 'sam': + ./${i}.bam + #else: + '$file' + #end if #end for - && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects - && mv *filt.sam dataset.filt.sam - && mv hicup_filter_summary* hicup_filter_summary.txt - && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam - && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam - && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam - && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam - && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam - && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam - #if $advanced_options.longest or $advanced_options.shortest: - && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam - #end if - - && mv *filter_piechart.svg filter_piechart.svg ]]></command> <inputs> - <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/> + <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/> <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> <section name="advanced_options" title="Advanced options"> <expand macro="filter_longest_shortest" /> </section> </inputs> <outputs> - <expand macro="filter_output" /> + <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> + <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> + <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> + <data name="re_ligation_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*re_ligation.filter.bam" label="re_ligation.filter.bam" /> + <data name="same_dangling_ends_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_dangling_ends.filter.bam" label="same_dangling_ends.filter.bam" /> + <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" /> + <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" /> + <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" /> + <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/> + <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> + <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> </outputs> <tests> <test> + <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" /> <param name="digest" value="digester_file.txt" ftype="txt" /> - <param name="inputFiles" value="result.pair.sam" ftype="sam" /> <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> - <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" /> - <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" /> - <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" /> - <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" /> - <output name="invalid_filter" file="dataset.invalid.filter.sam" lines_diff="8" /> - <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" /> - <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" /> - <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" /> + <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> + <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> + <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> </test> </tests> <help><![CDATA[