| Previous changeset 4:f4b429a3494a (2016-02-03) Next changeset 6:c50b7a3ff5ad (2016-02-04) |
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Commit message:
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty |
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modified:
STACKS_clone_filter.py STACKS_clone_filter.xml |
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| diff -r f4b429a3494a -r 1a5ebb16aaea STACKS_clone_filter.py --- a/STACKS_clone_filter.py Wed Feb 03 10:58:13 2016 -0500 +++ b/STACKS_clone_filter.py Thu Feb 04 07:50:26 2016 -0500 |
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| @@ -1,9 +1,11 @@ #!/usr/bin/python # -*- coding: utf-8 -*- -import shutil +import argparse +import glob +import os import subprocess -import argparse +import shutil def __main__(): @@ -20,10 +22,6 @@ os.mkdir('job_outputs') os.chdir('job_outputs') - # STACKS_archive - # check if zipped files are into the tab - extract_compress_files(options.P, os.getcwd()) - # create the populations command input line cmd_line=['clone_filter'] if options.f is not None: @@ -36,7 +34,7 @@ subprocess.call(cmd_line) # postprocesses - clean_files = glob.glob('*.fq') + clean_files = glob.glob('*.fq*') if options.f is not None: shutil.copy(clean_files[0], 'clean.fq') else: |
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| diff -r f4b429a3494a -r 1a5ebb16aaea STACKS_clone_filter.xml --- a/STACKS_clone_filter.xml Wed Feb 03 10:58:13 2016 -0500 +++ b/STACKS_clone_filter.xml Thu Feb 04 07:50:26 2016 -0500 |
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| @@ -34,6 +34,17 @@ <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> </when> </conditional> + <param name="oligo_len_1" type="int" label="length of the single-end oligo sequence in data set"/> + <param name="oligo_len_2" type="int" label="length of the paired-end oligo sequence in data set"/> + <param name="oligo_options" type="select" label="Oligo sequence options"> + <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option> + <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> + <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> + <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> + <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> + <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> + <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option> + </param> </inputs> <outputs> |