Mercurial > repos > lldelisle > cooler_cload_tabix
view cooler_cload_tabix.xml @ 4:168e86e96afa draft default tip
planemo upload for repository https://github.com/lldelisle/tools-lldelisle/blob/master/tools/cooler/.shed.yml commit bee0809b51b16e750353b19fad34bfcf5e93ab13
author | lldelisle |
---|---|
date | Tue, 02 Apr 2024 07:30:20 +0000 |
parents | 3ff6eeca667e |
children |
line wrap: on
line source
<tool id="cooler_cload_tabix" name="cooler_cload_tabix" version="@VERSION@+galaxy1" profile="22.05"> <description> Create a cool file from a tabix-indexed contact file and a list of genomic bins.</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command detect_errors="exit_code"><![CDATA[ ##set up input files ln -s '$format_sel.input_pairs' pairs.tabix && ln -s '$format_sel.input_pairs.metadata.tabix_index' pairs.tabix.tbi && cooler cload tabix --assembly '$assembly' #if $format_sel.format == "juicer_medium": -c2 7 -p2 8 #else: -c2 $format_sel.c2 -p2 $format_sel.p2 #end if '$input_bed' pairs.tabix '$output' ]]> </command> <inputs> <conditional name="format_sel"> <param name="format" type="select" label="Format of your input file"> <option value="juicer_medium">Juicer Medium Format</option> <option value="other">Other</option> </param> <when value="juicer_medium"> <param name="input_pairs" multiple="false" type="data" format="juicer_medium_tabix.gz" label="Select the output of csort_tabix."/> </when> <when value="other"> <param name="input_pairs" multiple="false" type="data" format="interval_tabix.gz" label="Select the output of csort_tabix."/> <param name="c2" type="integer" value="3" label="field number in the input file (starting from 1) of the chromosome of mate 2 (same as in csort)."> <validator type="in_range" min="1" /> </param> <param name="p2" type="integer" value="4" label="field number in the input file (starting from 1) of the position of mate 2 (same as in csort)."> <validator type="in_range" min="1" /> </param> </when> </conditional> <param name="assembly" type="text" label="name of genome assembly"/> <param name="input_bed" multiple="false" type="data" format="bed" label="Select the output of makebins."/> </inputs> <outputs> <data format="cool" name="output" label="cool file from $format_sel.input_pairs.name and $input_bed.name"/> </outputs> <tests> <test> <conditional name="format_sel"> <param name="format" value="juicer_medium"/> <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/> </conditional> <param name="input_bed" value="chr19.1M.bins"/> <param name="assembly" value="chr19"/> <output name="output" file="input.cool" compare="sim_size"/> </test> <test> <conditional name="format_sel"> <param name="format" value="other"/> <param name="input_pairs" value="input.validPairs.tabix" ftype="juicer_medium_tabix.gz"/> <param name="c2" value="7"/> <param name="p2" value="8"/> </conditional> <param name="input_bed" value="chr19.1M.bins"/> <param name="assembly" value="chr19"/> <output name="output" file="input.cool" compare="sim_size"/> </test> </tests> <help> **cooler cload** tool developped by mirnylab see https://github.com/open2c/cooler and https://cooler.readthedocs.io/en/latest/cli.html#cooler-cload-tabix command-line:: cooler cload tabix --assembly assembly -c2 c2 -p2 p2 input_bed input_pairs output </help> <expand macro="citation_cooler" /> </tool>