Mercurial > repos > thanhlv > biotradis
annotate biotradis_filter_tags.xml @ 1:eb1e9759c24e draft
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author | thanhlv |
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date | Thu, 25 Jul 2019 06:07:06 -0400 |
parents | afe9a515d145 |
children | 09c1f97a5bcc |
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afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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1 <tool id="filter_tradis_tags" name="filter tradis tags" version="@VERSION@"> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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2 <description>Filters a BAM file and outputs reads with tag matching -t option.</description> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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3 <macros> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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4 <import>macros.xml</import> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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5 </macros> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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6 <expand macro="requirements" /> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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7 <command detect_errors="exit_code"><![CDATA[ |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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8 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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9 filter_tradis_tags -b $input_bam -t $tag -m $mismatches -o filtered |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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10 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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11 ]]></command> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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12 <inputs> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff
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13 <param name="input_bam" type="data" format="bam" label="BAM file" help="" /> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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14 <param name="tag" type="text" label="Tags to filter" help="" /> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff
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15 <param name="mismatches" type="integer" value ="0" label="Number of mismatches to allow when matching tag" help="(optional. default = 0)" /> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff
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16 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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17 </inputs> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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18 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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19 <outputs> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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20 <data name="filtered_tags" format="fastq" label="${tool.name} on ${on_string}" from_work_dir="filtered.tag.fatsq" /> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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21 </outputs> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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22 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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23 <!-- <tests> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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24 </tests> --> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff
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25 <help><![CDATA[ |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
diff
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26 Adds transposon sequence and quality tags to the read strings and |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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27 outputs a BAM. |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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28 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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29 Usage: add_tags -b file.bam [options] |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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30 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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31 Options: |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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32 -b : bam file with tradis tags |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
parents:
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33 -v : verbose debugging output |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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34 ]]></help> |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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35 |
afe9a515d145
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
thanhlv
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36 </tool> |