Mercurial > repos > sanbi-uwc > qualimap2

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planemo upload for repository https://github.com/zipho/qualimap2 commit cdfee65aff3863f6477339300a4a11657d7a44c0
author sanbi-uwc
date Tue, 05 Apr 2016 06:06:54 -0400
parents 8dff744880cd
children
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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1 <?xml version="1.0" encoding="utf-8" ?>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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2 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="2.2">
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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3 <description>Tool to to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.</description>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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4 <requirements>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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5 <requirement type="package" version="2.2">qualimap</requirement>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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6 </requirements>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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7 <stdio>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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8 <exit_code range=":-1" />
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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9 <exit_code range="1:" />
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
parents:
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10 </stdio>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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11 <command interpreter="python">
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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12 qualimap_bamqc.py
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8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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13 --input_file $input_realigned_bam_file
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
parents: 4
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14 --out_genome_file $genomecov_file
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
parents: 4
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15 --out_dir $genomecov_file.files_path
8dff744880cd planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6
sanbi-uwc
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16 --java_mem_size $mem_size
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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17 </command>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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18 <inputs>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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19 <param name="input_realigned_bam_file" type="data" format="bam" label="Realigned BAM dataset" help="Specify realigned BAM dataset"/>
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dcd6ab7a3d8f planemo upload for repository https://github.com/zipho/qualimap2 commit 3835f1d76babcb2cce9b241fa77aeadad871e844
sanbi-uwc
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20 <param name="mem_size" type="text" value="8G" format="txt" label="Java memory size (default Gig)" help="Specify the size of memory to allocate. (Default 8 Gig)"/>
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d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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21 </inputs>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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22 <outputs>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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23 <data format="genomecov" name="genomecov_file" label="QualiMap: BamQC GenomeCov output"/>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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24 </outputs>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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25 <help>Help!</help>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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26 <citations>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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27 <citation></citation>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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28 </citations>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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29 <tests>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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30 <test>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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31 </test>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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32 </tests>
d87d6c0c27f5 planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0
sanbi-uwc
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33 </tool>