Mercurial > repos > bgruening > hicup_filter
diff hicup_filter.xml @ 0:566da23a5a08 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
| author | bgruening |
|---|---|
| date | Thu, 09 Mar 2017 09:31:25 -0500 |
| parents | |
| children | cfa9c047cda4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicup_filter.xml Thu Mar 09 09:31:25 2017 -0500 @@ -0,0 +1,68 @@ +<tool id="hicup_filter" name="Hicup Filter" version="0.1.0"> + <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' + #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 + #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 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" /> + </outputs> + <tests> + <test> + <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" /> + </test> + </tests> + <help><![CDATA[ + + For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ + + To get more information about the filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter + ]]></help> + <expand macro="citation_hicup" /> +</tool>