Mercurial > repos > cmonjeau > mapsembler2
changeset 2:5aea5b993ae8
fix .dat unknown extension for kissreads
| author | cmonjeau |
|---|---|
| date | Fri, 11 Sep 2015 10:04:40 +0000 |
| parents | f7458a23cebe |
| children | c62c5fd56ebf |
| files | mapsembler2.py mapsembler2.xml |
| diffstat | 2 files changed, 17 insertions(+), 11 deletions(-) [+] |
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--- a/mapsembler2.py Mon Jul 06 15:53:45 2015 +0000 +++ b/mapsembler2.py Fri Sep 11 10:04:40 2015 +0000 @@ -12,7 +12,7 @@ http://www.irisa.fr/symbiose/people/ppeterlongo/mapsembler2_2.2.3.zip -or with the galaxy_mapsembler2 package in the GenOuest toolshed +or with the package_mapsembler2_2_2_3 package in the GUGGO toolshed and main toolshed """ @@ -49,8 +49,13 @@ #inputs cmd_line.append("-r") - #cmd_line.append(inputs) - cmd_line.append(' '.join(options.input_files.split(","))) + inputs_tab = [] + + for input in options.input_files.split(","): + os.symlink(input, os.path.basename(input)+'.'+options.extension_format) + inputs_tab.append(os.path.basename(input)+'.'+options.extension_format) + + cmd_line.append(' '.join(inputs_tab)) # add parameters into the command line cmd_line.extend(["-t", options.output_extension, "-k", options.kmer, "-c", options.coverage, "-d", options.substitutions, "-g", options.genome_size, "-f", options.process_search, "-x", options.max_length, "-y", options.max_depth]) @@ -59,15 +64,8 @@ log = open(options.output, "w") log.write("[COMMAND LINE] "+' '.join(cmd_line)) - process=subprocess.Popen(cmd_line, - stdout=subprocess.PIPE, stderr=subprocess.PIPE) - - stdoutput, stderror = process.communicate() + process=subprocess.call(cmd_line) - # results recuperation - log.write(stdoutput) - log.write(stderror) - # close log file log.close()
--- a/mapsembler2.xml Mon Jul 06 15:53:45 2015 +0000 +++ b/mapsembler2.xml Fri Sep 11 10:04:40 2015 +0000 @@ -7,6 +7,7 @@ mapsembler2.py -s $input_starters -r $data_files +-e $extension_format -t $output_extension -k $kmer -c $coverage @@ -23,6 +24,10 @@ <!-- Input data files --> <param name="input_starters" type="data" format="fasta" label="Starters" help="set of input sequences" /> <param name="data_files" type="data" multiple="true" format="fasta,fastq" label="Read file" help="Data loaded in the script" /> + <param name="extension_format" type="select" label="Input files"> + <option value="fasta">fasta</option> + <option value="fastq">fastq</option> + </param> <param name="output_extension" type="select" label="Select your output extension type"> <option value="1">a strict sequence</option> <option value="2">a consensus sequence</option> @@ -48,6 +53,9 @@ </data> </outputs> + <stdio> + <exit_code range="1" level="fatal" description="Error in Stacks Denovo execution" /> + </stdio> <help> **Description**