Mercurial > repos > iuc > circexplorer2

annotate macros.xml @ 0:581c89681b37 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
author iuc
date Fri, 26 Aug 2022 22:42:55 +0000
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581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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1 <macros>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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2 <token name="@TOOL_VERSION@">2.3.8</token>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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3 <token name="@VERSION_SUFFIX@">0</token>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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4 <xml name="requirements">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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5 <requirements>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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6 <requirement type="package" version="@TOOL_VERSION@">circexplorer2</requirement>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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7 </requirements>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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8 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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9 <xml name="xrefs">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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10 <xrefs>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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11 <xref type="bio.tools">circexplorer2</xref>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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12 </xrefs>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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13 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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14 <xml name="parse_fusion" token_format="" token_label="" token_help="">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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15 <param name="fusion_file" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP@"/>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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16 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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17 <xml name="parse_statistics">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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18 <param argument="-f" type="boolean" truevalue="-f" falsevalue="" checked="false"
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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19 label="Statistics fragment numbers rather than read numbers"/>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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20 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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21 <xml name="genome_file">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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22 <param argument="--genome" type="data" format="fasta" label="Reference genome" help="In FASTA format"/>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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23 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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24 <xml name="annotation_file">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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25 <param argument="--ref" type="data" format="txt" label="Gene annotation"
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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26 help="The file is in the format of Gene Predictions and RefSeq Genes with Gene Names" />
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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27 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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28 <xml name="junction_file">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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29 <param argument="--bed" type="data" format="bed" label="Back spliced junction file"
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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30 help="This file can be created by CIRCexplorer2 parse or CIRCexplorer2 align" />
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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31 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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32 <xml name="tophat_file">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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33 <param argument="--tophat" type="data" format="tgz" label="TopHat alignment file"
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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34 help="Generated by the align module" />
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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35 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
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36 <token name="@threads@"><![CDATA[--thread=\${GALAXY_SLOTS:-10}]]></token>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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37 <xml name="citations">
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
iuc
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38 <citations>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
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39 <citation type="doi">10.1101/gr.202895.115</citation>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
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40 </citations>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
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41 </xml>
581c89681b37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/circexplorer2 commit fe03991cd7c43f5266314d1fb9e4108f1ab102e8
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42 </macros>