Mercurial > repos > mvdbeek > bam_readtagger

annotate allow_dovetailing.xml @ 2:39d9bc17ec74 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit b0627386ac1cc004dc71fc788bf37111213b1fab-dirty
author mvdbeek
date Fri, 17 Feb 2017 12:55:58 -0500
parents f69131f584e8
children cb9036583afe
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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39d9bc17ec74 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit b0627386ac1cc004dc71fc788bf37111213b1fab-dirty
mvdbeek
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1 <tool id="allow_dovetailing" name="Allow dovetailing" version="0.1.13">
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mvdbeek
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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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39d9bc17ec74 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit b0627386ac1cc004dc71fc788bf37111213b1fab-dirty
mvdbeek
parents: 1
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4 <requirement type="package" version="0.1.13">readtagger</requirement>
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a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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5 </requirements>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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6 <command detect_errors="aggressive"><![CDATA[
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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7 allow_dovetailing -i '$input' -o '$output'
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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8 ]]></command>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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9 <inputs>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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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>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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16 <test>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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
mvdbeek
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21 <help><![CDATA[
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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22 ::
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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23 usage: allow_dovetailing [-h] -i INPUT_PATH -o OUTPUT_PATH
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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24
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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25 Allow dovetailing.
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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26
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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27 optional arguments:
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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28 -h, --help show this help message and exit
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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29 -i INPUT_PATH, --input_path INPUT_PATH
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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30 Input alignment file to manipulate
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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31 -o OUTPUT_PATH, --output_path OUTPUT_PATH
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
mvdbeek
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32 Output alignment file
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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33 ]]></help>
a38447a59412 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit d63500891dc173a7657bb9a9aabbeb6cf2ddb9e3-dirty
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34 </tool>