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annotate alignment_size_distribution.xml @ 4:f1eeaf42144b draft default tip

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planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit c8e0a703fcdff580ba0a0c5806a37c088c03ab7b-dirty
author mvdbeek
date Mon, 20 Aug 2018 14:46:57 -0400
parents 21b5a9170b90
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ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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1 <tool id="alignment_size_distribution" name="Create size distribution for alignment files" version="0.1.0">
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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2 <requirements>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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3 <requirement type="package" version="6.7">click</requirement>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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4 <requirement type="package" version="0.23">pandas</requirement>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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5 <requirement type="package" version="0.15">pysam</requirement>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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6 </requirements>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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7 <command detect_errors="exit_code"><![CDATA[
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3ed18dcb6f82 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit a0c9f33672103cf29ad015477ebb898007ba9ae8
mvdbeek
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8 python '$__tool_directory__/size_distributions.py' '$alignment_file' --minimum_size $minimum_size --maximum_size $maximum_size $wide --output '$distribution'
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ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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9 ]]></command>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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10 <inputs>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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11 <param name="alignment_file" type="data" format="bam,unsorted.bam"/>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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12 <param argument="--minimum_size" type="integer" value="18" min="1" label="Minimum read length to consider"/>
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21b5a9170b90 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit c8e0a703fcdff580ba0a0c5806a37c088c03ab7b
mvdbeek
parents: 2
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13 <param argument="--maximum_size" type="integer" value="30" min="1" label="Maximum read length to consider"/>
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c8c7b6113241 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit a0c9f33672103cf29ad015477ebb898007ba9ae8-dirty
mvdbeek
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14 <param argument="--wide" type="boolean" checked="false" truevalue="--wide" falsevalue="--long" label="Output wide instead of long tabular format"/>
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ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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15 </inputs>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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16 <outputs>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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17 <data name="distribution" format="tabular"/>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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18 </outputs>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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19 <tests>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
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20 <test>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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21 <param name="alignment_file" value="test_data.bam" ftype="bam"/>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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22 <output name="distribution" value="distribution.tab" ftype="tabular"/>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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23 </test>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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24 </tests>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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25 <help><![CDATA[
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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26 Generates a table with reference sequence, sense and antisense counts.
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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27 ]]></help>
ac5584567084 planemo upload for repository https://github.com/bardin-lab/smallRNA_tools commit 48d9f377e28d686c2e0d8eee6684e34c52b7b3cc
mvdbeek
parents:
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28 </tool>