| Previous changeset 5:909c315b656d (2017-03-01) Next changeset 7:9006e5836729 (2017-10-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 6704655441902c44ee5c782578fe4c487cff6340 |
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modified:
spades.xml |
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| diff -r 909c315b656d -r 65c2d63fcbe6 spades.xml --- a/spades.xml Wed Mar 01 15:33:26 2017 -0500 +++ b/spades.xml Sat May 13 15:51:58 2017 -0400 |
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| @@ -70,6 +70,8 @@ --untrusted-contigs $contig.extension:$contig #end if #end for + && cat contigs.fasta | python '$write_tsv_script' > '$out_contig_stats' + && cat scaffolds.fasta | python '$write_tsv_script' > '$out_scaffold_stats' ]]> </command> <inputs> @@ -141,7 +143,31 @@ <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" /> <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" /> </inputs> + <configfiles> + <configfile name="write_tsv_script"><![CDATA[#!/usr/bin/env python +import sys,re +search_str = r'^>(NODE|\S+)_(\d+)(?:_|\s)length_(\d+)_cov_(\d+\.*\d*).*\$' +replace_str = r'\1_\2\t\3\t\4' +cmd = re.compile(search_str) +sys.stdout.write('#name\tlength\tcoverage\n') +for i,line in enumerate(sys.stdin): + if cmd.match(line): + sys.stdout.write(cmd.sub(replace_str,line)) +]]> + </configfile> + </configfiles> + <outputs> + <data format="tabular" label="SPAdes contig stats" name="out_contig_stats" > + <actions> + <action name="column_names" type="metadata" default="name,length,coverage"/> + </actions> + </data> + <data format="tabular" label="SPAdes scaffold stats" name="out_scaffold_stats" > + <actions> + <action name="column_names" type="metadata" default="name,length,coverage"/> + </actions> + </data> <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" /> <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" /> <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" /> @@ -155,6 +181,11 @@ <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" /> <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" /> <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" /> + <output name="out_contig_stats"> + <assert_contents> + <has_text_matching expression="NODE_1\t1000\t225"/> + </assert_contents> + </output> </test> <test> <param name="sc" value="false" /> |