Mercurial > repos > drosofff > msp_sr_bowtie
changeset 7:5d82f9b15957 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Tue, 23 Jun 2015 16:59:01 -0400 |
| parents | 738a39851eae |
| children | 67a7d18a3065 |
| files | sRbowtie.py sRbowtie.xml |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/sRbowtie.py Thu Jun 11 09:22:04 2015 -0400 +++ b/sRbowtie.py Tue Jun 23 16:59:01 2015 -0400 @@ -145,7 +145,7 @@ # |samtools view -bS -o /tmp/tmp_PgMT0/unsorted.bam - # generates an "unsorted.bam.sorted.bam file", NOT an # "unsorted.bam.sorted" file - second_command_line = "/usr/bin/env samtools sort %s %s" % ( + second_command_line = "samtools sort %s %s" % ( path_to_unsortedBam, path_to_sortedBam) # fileno() method return the file descriptor number of tmp_stderr p = subprocess.Popen(
--- a/sRbowtie.xml Thu Jun 11 09:22:04 2015 -0400 +++ b/sRbowtie.xml Tue Jun 23 16:59:01 2015 -0400 @@ -55,12 +55,12 @@ </when> </conditional> <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select"> - <option select="true" value="tabular">tabular</option> + <option selected="true" value="tabular">tabular</option> <option value="sam">sam</option> <option value="bam">bam</option> </param> <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select"> - <option select="true" value="No">No</option> + <option selected="true" value="No">No</option> <option value="al">aligned</option> <option value="unal">unaligned</option> <option value="al_and_unal">both aligned and unaligned</option>