Mercurial > repos > jjohnson > contig_annotation_tool
diff cat_bins.xml @ 0:ad7507073c3f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
| author | jjohnson |
|---|---|
| date | Sun, 24 Nov 2019 21:56:00 -0500 |
| parents | |
| children | 86cd2e70b0dc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cat_bins.xml Sun Nov 24 21:56:00 2019 -0500 @@ -0,0 +1,71 @@ +<tool id="cat_bins" name="CAT bins" version="@VERSION.0"> + <description>annotate with taxonomic classification</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #set $bin_dir = None + #if len($mags) > 1: + #set $bin_dir = 'inputs' + mkdir -p $bin_dir && + #for mag in $mags: + ln -s '$mag' $bin_dir/ && + #end for + #end if + CAT + #if $bin_dir + bins -s '.dat' -b $bin_dir + #else + bin -b '$mags' + #end if + @CAT_DB@ + @USE_INTERMEDIATES@ + @CUSTOM_SETTINGS@ + && @TXT2TSV@ *.ORF2LCA.txt *.bin2classification.txt + @ADD_NAMES@ + @SUMMARISE@ + ]]></command> + <inputs> + <param name="mags" type="data" format="fasta" multiple="true" label="metagenome assembled genomes (MAGs/bins)"/> + <expand macro="cat_db" /> + <expand macro="use_intermediates" /> + <expand macro="custom_settings" /> + <expand macro="add_names" /> + <expand macro="summarise" /> + <expand macro="select_bat_outputs" /> + </inputs> + <outputs> + <expand macro="outputs" /> + </outputs> + <tests> + <test> + <param name="mags" ftype="fasta" value="genome3.fna"/> + <expand macro="test_catdb"/> + <param name="select_outputs" value="contig2classification"/> + <output name="contig2classification"> + <assert_contents> + <has_text text="1639" /> + </assert_contents> + </output> + </test> + <param name="mags" ftype="fasta" value="genome2.fna,genome3.fna"/> + <expand macro="test_catdb"/> + <param name="select_outputs" value="contig2classification"/> + <output name="contig2classification"> + <assert_contents> + <has_text text="666" /> + <has_text text="1639" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +**CAT bin or bins** +Classify metagenomics assembled genomes. + +@COMMON_HELP@ + ]]></help> + <expand macro="citations" /> +</tool>