Mercurial > repos > bgruening > infernal
diff cmscan.xml @ 8:c9e29ac5d099 draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
author | bgruening |
---|---|
date | Thu, 23 Sep 2021 19:38:58 +0000 |
parents | 6e18e0b098cd |
children |
line wrap: on
line diff
--- a/cmscan.xml Sat Nov 11 16:01:09 2017 -0500 +++ b/cmscan.xml Thu Sep 23 19:38:58 2021 +0000 @@ -1,10 +1,11 @@ -<tool id="infernal_cmscan" name="cmscan" version="@VERSION@.0"> +<tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description> Search sequences against collections of covariance models</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> + <expand macro="xrefs"/> <command> <![CDATA[ ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy @@ -73,8 +74,19 @@ #end if ## sequence file '$seqdb' - && - sed 's/ \+ /\t/g' '\$temp_tabular_output' > '$outfile' + ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984 + ## remove the header + && tail -n +3 '\$temp_tabular_output' > headless_file + ## extract the last column, since the description includes a variable number of spaces (so, is not considered as a column by awk) + && awk '{$1=$2=$3=$4=$5=$6=$7=$8=$9=$10=$11=$12=$13=$14=$15=$16=$17=""; print $0}' headless_file > description_column + ## fix the tabulation the rest content (except the description column) + && awk 'OFS="\t" {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17 > ("tabulated_columns")}' headless_file + ## add the description column to the tabulated data + && paste -d"\t" tabulated_columns description_column > joined_file + ## include a correct header + && echo -e '#target\tname\taccession\tquery name\taccession\tmdl\tmdl from\tmdl to\tseq from\tseq to\tstrand\ttrunc\tpass\tgc\tbias\tscore\tE-value\tinc\tdescription of target' > header + ## export the result + && cat header joined_file > '$outfile' ]]> </command> @@ -226,12 +238,10 @@ label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/> </section> - - - </inputs> <outputs> <data format="tabular" name="outfile" label="cmscan on ${on_string}"/> + </outputs> <tests> <test> @@ -241,8 +251,9 @@ </conditional> <param name="aux_files" value="minifam.tar" ftype="tar"/> <param name="seqdb" value="metag-example.fa"/> - <output name="outfile"> + <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8"> <assert_contents> + <has_n_lines n="15"/> <has_text text="AAGA01015927.1"/> </assert_contents> </output>