Mercurial > repos > mvdbeek > damidseq_core

annotate patch @ 4:b07936a3962d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
author mvdbeek
date Sun, 26 Mar 2017 15:53:05 -0400
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4
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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diff changeset
1 diff -r e47f77820200 damidseq_core.xml
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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2 --- a/damidseq_core.xml Sun Mar 26 10:31:55 2017 -0400
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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3 +++ b/damidseq_core.xml Sun Mar 26 21:49:38 2017 +0200
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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4 @@ -5,8 +5,8 @@
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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5 </requirements>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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7 <command detect_errors="aggressive"><![CDATA[
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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8 - ln -f -s '$dam' A001.fastq &&
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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9 ln -f -s '$dam_fusion' A002.fastq &&
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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10 + ln -f -s '$dam_only' A001.fastq &&
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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11 ln -f -s '$index' index.txt &&
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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12 HOME="\$PWD" damidseq_pipeline
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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13 --bins=$bins
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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14 @@ -36,7 +36,7 @@
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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15 </configfiles>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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16 <inputs>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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17 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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18 - <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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19 + <param name="dam_only" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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20 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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21 <options from_data_table="bowtie2_indexes">
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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22 <filter type="sort_by" column="2"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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23 @@ -106,8 +106,8 @@
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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24 </outputs>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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25 <tests>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
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26 <test>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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27 - <param name="dam" value="A001.fastq"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
diff changeset
28 <param name="dam_fusion" value="A002.fastq"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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29 + <param name="dam_only" value="A001.fastq"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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30 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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31 <param name="reference_index" value="dm6"/>
b07936a3962d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 077b3265c7a67b999daa820e13888991b15a98a1
mvdbeek
parents:
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32 <param name="norm_method" value="rpm"/>