Mercurial > repos > mvdbeek > bam_readtagger

annotate allow_dovetailing.xml @ 9:53b71263e2a2 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
author mvdbeek
date Wed, 08 Mar 2017 05:14:25 -0500
parents bf8ffb337cbe
children c179d081b6ba
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53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents: 8
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1 <tool id="allow_dovetailing" name="Allow dovetailing" version="0.3.5">
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2 <description>modifies proper_pair flag in bam files</description>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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3 <requirements>
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53b71263e2a2 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty
mvdbeek
parents: 8
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4 <requirement type="package" version="0.3.5">readtagger</requirement>
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5 </requirements>
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mvdbeek
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6 <command detect_errors="aggressive"><![CDATA[
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7 allow_dovetailing -i '$input' -o '$output'
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mvdbeek
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8 ]]></command>
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mvdbeek
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9 <inputs>
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mvdbeek
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10 <param name="input" argument="--input_path" type="data" format="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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11 </inputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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12 <outputs>
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13 <data name="output" format="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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14 </outputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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15 <tests>
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16 <test>
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mvdbeek
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17 <param name="input" value="not_a_proper_pair.bam" ftype="bam"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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18 <output name="output" file="proper_pair.bam" ftype="bam" lines_diff="2"/>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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19 </test>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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20 </tests>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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21 <help><![CDATA[
3
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mvdbeek
parents: 2
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22 .. code-block::
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23
3
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mvdbeek
parents: 2
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24 usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH
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mvdbeek
parents: 2
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25
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mvdbeek
parents: 2
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26 Allow dovetailing.
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27
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mvdbeek
parents: 2
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28 optional arguments:
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mvdbeek
parents: 2
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29 -h, --help show this help message and exit
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mvdbeek
parents: 2
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30 -i INPUT_PATH, --input_path INPUT_PATH
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
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31 Input alignment file to manipulate
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mvdbeek
parents: 2
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32 -o OUTPUT_PATH, --output_path OUTPUT_PATH
cb9036583afe planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit e9d18b939a9172b858c178e6bb4ef9ce2138c94c-dirty
mvdbeek
parents: 2
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33 Output alignment file
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34 ]]></help>
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35 </tool>