Mercurial > repos > lparsons > rseqc
changeset 1:cd2daa987b69 draft default tip
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc commit 2400cce6e3918648fda8f2a8d8485ab251a58827
| author | lparsons |
|---|---|
| date | Tue, 07 Jul 2015 14:14:04 -0400 |
| parents | 306127635959 |
| children | |
| files | bam_stat.xml clipping_profile.xml geneBody_coverage.xml |
| diffstat | 3 files changed, 12 insertions(+), 11 deletions(-) [+] |
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--- a/bam_stat.xml Tue Jul 07 10:39:47 2015 -0400 +++ b/bam_stat.xml Tue Jul 07 14:14:04 2015 -0400 @@ -17,13 +17,13 @@ <version_command><![CDATA[bam_stat.py --version]]></version_command> <command><![CDATA[ - bam_stat.py -i $input -q $mapqual 2> $output + bam_stat.py -i $input -q $mapq 2> $output ]]> </command> <inputs> - <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> - <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" /> + <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> + <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" /> </inputs> <outputs> @@ -42,7 +42,8 @@ +++++++++++ This program is used to calculate reads mapping statistics from provided BAM -file. This script determines "uniquely mapped reads" from `mapping quality`_, +file. This script determines "uniquely mapped reads" from `mapping quality +<http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_, which quality the probability that a read is misplaced (Do NOT confused with sequence quality, sequence quality measures the probability that a base-calling was wrong) . @@ -54,7 +55,7 @@ Alignment file in BAM/SAM format. Minimum mapping quality - Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30) + Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30) Output ++++++++++++++
--- a/clipping_profile.xml Tue Jul 07 10:39:47 2015 -0400 +++ b/clipping_profile.xml Tue Jul 07 14:14:04 2015 -0400 @@ -23,7 +23,7 @@ </command> <inputs> - <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> + <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> </inputs> <outputs>
--- a/geneBody_coverage.xml Tue Jul 07 10:39:47 2015 -0400 +++ b/geneBody_coverage.xml Tue Jul 07 14:14:04 2015 -0400 @@ -36,12 +36,12 @@ </command> <inputs> - <param name="input" type="data" label="Additional input .bam files" format="bam" /> - <repeat name="additionalinputs" title="Input .bam file"> - <param name="file" type="data" label="Input .bam file" format="bam" /> + <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/> + <repeat name="additionalinputs" title="Additional input .bam files"> + <param name="file" type="data" label="Additional input .bam file" format="bam" /> </repeat> - <param name="refgene" type="data" label="Reference Genome" format="bed" /> - <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length" help="Minimum mRNA length (bp). mRNA that are shorter than this value will be skipped (default is 100)." /> + <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/> + <param name="minimum_length" type="integer" value="100" label="Minimum mRNA length in bp (default: 100)" help="mRNA that are shorter than this value will be skipped (--minimum_length)." /> </inputs> <outputs>