Mercurial > repos > mvdbeek > bam_readtagger
annotate write_supplementary_fastq.xml @ 27:9f7737be4732 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 49b0c7b7499bb6ec64ca1d4fa3ef427b071604d7-dirty
author | mvdbeek |
---|---|
date | Fri, 28 Apr 2017 02:16:42 -0400 |
parents | 1d71664174d9 |
children | be95c9c82937 |
rev | line source |
---|---|
27
9f7737be4732
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 49b0c7b7499bb6ec64ca1d4fa3ef427b071604d7-dirty
mvdbeek
parents:
26
diff
changeset
|
1 <tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.21"> |
9
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
2 <description>from SAM/BAM alignment files as FASTQ</description> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
3 <requirements> |
27
9f7737be4732
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 49b0c7b7499bb6ec64ca1d4fa3ef427b071604d7-dirty
mvdbeek
parents:
26
diff
changeset
|
4 <requirement type="package" version="0.3.21">readtagger</requirement> |
9
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
5 </requirements> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
6 <version_command>write_supplementary_fastq --version</version_command> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
7 <command detect_errors="aggressive"><![CDATA[ |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
8 write_supplementary_fastq --input_path '$input' --output_path '$output' |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
9 ]]></command> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
10 <inputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
11 <param name="input" argument="--input_path" type="data" format="bam"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
12 </inputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
13 <outputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
14 <data name="output" format="fastqsanger"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
15 </outputs> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
16 <tests> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
17 <test> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
18 <param name="input" value="supplementary.bam" ftype="bam"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
19 <output name="output" file="supplementary.fastq" ftype="fastqsanger"/> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
20 </test> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
21 </tests> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
22 <help><![CDATA[ |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
23 .. code-block:: |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
24 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
25 Usage: write_supplementary_fastq [OPTIONS] |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
26 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
27 Write all supplementary alignments in `input_path` to an output fastq file |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
28 at `output_path`. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
29 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
30 Options: |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
31 --input_path PATH Collect supplementary reads in this alignment file. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
32 --output_path PATH Write supplementary reads to this FASTQ file. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
33 --help Show this message and exit. |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
34 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
35 |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
36 ]]></help> |
53b71263e2a2
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents:
diff
changeset
|
37 </tool> |