Mercurial > repos > iuc > bcftools_plugin_counts
view bcftools_plugin_counts.xml @ 18:97e8145d7e30 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 087a38fc2eade9f3a286d672ba61571b0b69a797
author | iuc |
---|---|
date | Mon, 26 Sep 2022 18:26:35 +0000 |
parents | f7879f1e77f9 |
children | dadbd61dc4cf |
line wrap: on
line source
<?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>plugin counts number of samples, SNPs, INDELs, MNPs and total sites</description> <macros> <token name="@EXECUTABLE@">counts</token> <token name="@PLUGIN_ID@">counts</token> <import>macros.xml</import> </macros> <expand macro="bio_tools" /> <expand macro="requirements"> <requirement type="package" version="3.7">python</requirement> </expand> <expand macro="version_command" /> <command detect_errors="aggressive"><![CDATA[ @PREPARE_ENV@ @PREPARE_INPUT_FILE@ #set $section = $sec_restrict @PREPARE_TARGETS_FILE@ @PREPARE_REGIONS_FILE@ bcftools plugin @EXECUTABLE@ ## VCF input section #set $section = $sec_restrict @INCLUDE@ @EXCLUDE@ @REGIONS@ @TARGETS@ ## Primary Input/Outputs @INPUT_FILE@ | tee counts_file.txt && sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > '$output_file' ]]> </command> <configfiles> <configfile name="transform"><![CDATA[ from __future__ import print_function import sys header = [] value = [] for line in sys.stdin: h,v = line.strip().split() header.append(h) value.append(v) print( '#%s' % '\t'.join(header) ) print( '%s' % '\t'.join(value) ) ]]> </configfile> </configfiles> <inputs> <expand macro="macro_input" /> <section name="sec_restrict" expanded="false" title="Restrict to"> <expand macro="macro_restrict" /> <expand macro="macro_restrict" type="target" label_type="Target" /> <expand macro="macro_include" /> <expand macro="macro_exclude" /> </section> </inputs> <outputs> <data name="output_file" format="tabular"/> </outputs> <tests> <test> <param name="input_file" ftype="vcf" value="view.vcf" /> <output name="output_file"> <assert_contents> <has_text text="SNPs"/> <has_text text="11"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ ===================================== bcftools @EXECUTABLE@ plugin ===================================== Counts number of samples, SNPs, INDELs, MNPs and total number of sites. @REGIONS_HELP@ @TARGETS_HELP@ @EXPRESSIONS_HELP@ ]]></help> <expand macro="citations" /> </tool>