annotate split.xml @ 2:53d73d58e105 draft

planemo upload for repository https://github.com/open2c/pairtools commit edb9fd7a6734203070b623876e76ce4a0a164ed9
author iuc
date Tue, 16 Apr 2024 12:50:54 +0000
parents bffcba7ce9b5
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bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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1 <tool id="pairtools_split" name="Pairtools split" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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2 <description>Split a pairsam file into pairs and SAM/BAM</description>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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3 <macros>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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4 <import>macros.xml</import>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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5 </macros>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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6 <expand macro="requirements"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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7 <command detect_errors="exit_code"><![CDATA[
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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8 pairtools split
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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9 '$pairsam_path'
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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10 --output-pairs '$output_pairs'
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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11 --output-sam ./output.bam
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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12 --nproc-in \${GALAXY_SLOTS:-4}
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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13 --nproc-out \${GALAXY_SLOTS:-4}
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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14 ]]></command>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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15 <inputs>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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16 <param name="pairsam_path" type="data" format="4dn_pairsam" label="Input 4dn pairsam file"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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17 </inputs>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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18 <outputs>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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19 <data name="output_pairs" format="4dn_pairs" label="${tool.name} on ${on_string}: Output Pairs" />
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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20 <data name="output_file" format="qname_sorted.bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: Output BAM" />
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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21 </outputs>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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22 <tests>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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23 <!--Test default parameters-->
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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24 <test expect_num_outputs="2">
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
iuc
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25 <param name="pairsam_path" value="output_dedup_pairs_markdups.pairsam"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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26 <output name="output_pairs" ftype="4dn_pairs" file="output_pairs_split.pairs" lines_diff="10"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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27 <output name="output_file" ftype="qname_sorted.bam" file="output_pairs_split.bam" lines_diff="20"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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28 </test>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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29 </tests>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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30 <help><![CDATA[
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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31 **Pairtools split**
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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32
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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33 Restore a SAM/BAM file from SAM1 and SAM2 fields of a `pairsam` file. Create a `pairs` file without SAM1/SAM2 fields.
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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34
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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35 ]]></help>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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36 <expand macro="citations"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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37 <expand macro="creator"/>
bffcba7ce9b5 planemo upload for repository https://github.com/open2c/pairtools commit 33081628e25ae7ace6d357c8f22994825f8fc428
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38 </tool>