Mercurial > repos > bgruening > text_processing
changeset 17:f46f0e4f75c4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 5f5d5802a961a77ceb092cbdef90d93e29717029-dirty"
| author | bgruening |
|---|---|
| date | Tue, 22 Jun 2021 16:06:48 +0000 |
| parents | ddf54b12c295 |
| children | d698c222f354 |
| files | cat.xml sort_rows.xml unfold_column.py |
| diffstat | 3 files changed, 21 insertions(+), 14 deletions(-) [+] |
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--- a/cat.xml Tue Oct 06 09:47:04 2020 +0000 +++ b/cat.xml Tue Jun 22 16:06:48 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="tp_cat" name="Concatenate datasets" version="0.1.0"> +<tool id="tp_cat" name="Concatenate datasets" version="0.1.1"> <description>tail-to-head (cat)</description> <macros> <import>macros.xml</import> @@ -11,12 +11,15 @@ </version_command> <command> <![CDATA[ - cat - #echo ' '.join(['"%s"' % $file for $file in $inputs])# + #for $file in $inputs: + cat '$file' >> '$out_file1' && + #end for #for $q in $queries: - #echo ' '.join(['"%s"' % $file for $file in $q.inputs2])# + #for $file in $q.inputs2: + cat '$file' >> '$out_file1' && + #end for #end for - > $out_file1 + exit 0 ]]></command> <inputs> <param name="inputs" multiple="true" type="data" format="txt,fastq.gz,fasta.gz,genbank.gz,tabular.gz" label="Datasets to concatenate"/>
--- a/sort_rows.xml Tue Oct 06 09:47:04 2020 +0000 +++ b/sort_rows.xml Tue Jun 22 16:06:48 2021 +0000 @@ -1,11 +1,11 @@ -<tool id="tp_sort_rows" name="Sort a row" version="@BASE_VERSION@.0"> +<tool id="tp_sort_rows" name="Sort a row" version="@BASE_VERSION@.0+galaxy0"> <description>according to their columns</description> <macros> <import>macros.xml</import> </macros> <command> <![CDATA[ - python -c 'for line in ( "\t".join(sorted(line.strip().split("\t"))) for line in open("$infile") ): print line' > $outfile + python -c 'for line in ( "\t".join(sorted(line.strip().split("\t"))) for line in open("$infile") ): print(line)' > $outfile ]]> </command> <inputs>
--- a/unfold_column.py Tue Oct 06 09:47:04 2020 +0000 +++ b/unfold_column.py Tue Jun 22 16:06:48 2021 +0000 @@ -2,18 +2,22 @@ import sys -out = open(sys.argv[4], 'w+') +out = open(sys.argv[4], "w+") sep = sys.argv[3] # un-sanitize Galaxy inputs -if sep == 'X': - sep = ';' +if sep == "X": + sep = ";" with open(sys.argv[1]) as handle: for line in handle: - cols = line.split('\t') + cols = line.split("\t") unfolding_column = int(sys.argv[2]) - 1 - column_content = cols[ unfolding_column ] - for elem in column_content.split( sep ): - out.write( '\t'.join( cols[:unfolding_column] + [elem] + cols[unfolding_column+1:]) ) + column_content = cols[unfolding_column] + for elem in column_content.split(sep): + out.write( + "\t".join( + cols[:unfolding_column] + [elem] + cols[unfolding_column + 1:] + ) + ) out.close()