Mercurial > repos > thanhlv > biotradis
comparison biotradis_filter_tags.xml @ 7:09c1f97a5bcc draft
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
author | thanhlv |
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date | Fri, 06 Dec 2019 10:11:20 -0500 |
parents | afe9a515d145 |
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6:5506c4307812 | 7:09c1f97a5bcc |
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6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <command detect_errors="exit_code"><![CDATA[ | 7 <command detect_errors="exit_code"><![CDATA[ |
8 | 8 |
9 filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered | 9 filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered |
10 | 10 |
11 ]]></command> | 11 ]]> </command> |
12 <inputs> | 12 <inputs> |
13 <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> | 13 <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> |
14 <param name="tag" type="text" label="Tags to filter" help="" /> | 14 <param name="tag" type="text" label="Tags to filter" help="" /> |
15 <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> | 15 <param name="mismatches" type="integer" min="0" value ="0" label="Number of mismatches to allow when matching tag" /> |
16 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> | 16 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" /> |
17 </inputs> | 17 </inputs> |
18 | 18 |
19 <outputs> | 19 <outputs> |
20 <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" /> | 20 <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" /> |
21 </outputs> | 21 </outputs> |
22 | 22 |
23 <!-- <tests> | 23 <!-- <tests> |
24 </tests> --> | 24 </tests> --> |
25 <help><![CDATA[ | 25 <help><![CDATA[ |
29 Usage: add_tags -b file.bam [options] | 29 Usage: add_tags -b file.bam [options] |
30 | 30 |
31 Options: | 31 Options: |
32 -b : bam file with tradis tags | 32 -b : bam file with tradis tags |
33 -v : verbose debugging output | 33 -v : verbose debugging output |
34 ]]></help> | 34 ]]> </help> |
35 <expand macro="citations" /> | |
35 | 36 |
36 </tool> | 37 </tool> |