Mercurial > repos > bgruening > deeptools_alignmentsieve

comparison deepTools_macros.xml @ 4:b2e9d7fbca60 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a
author bgruening
date Wed, 22 Aug 2018 17:33:05 -0400
parents 11f1d6fcf2c2
children 0bac1f03ef5d
comparison
equal deleted inserted replaced
3:11f1d6fcf2c2 4:b2e9d7fbca60
1 <macros> 1 <macros>
2 2
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 <token name="@WRAPPER_VERSION@">3.1.0</token> 4 <token name="@WRAPPER_VERSION@">3.1.2.0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.1.0">deeptools</requirement> 7 <requirement type="package" version="3.1.2">deeptools</requirement>
8 <requirement type="package" version="1.7">samtools</requirement> 8 <requirement type="package" version="1.7">samtools</requirement>
9 </requirements> 9 </requirements>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <version_command>@BINARY@ --version</version_command> 11 <version_command>@BINARY@ --version</version_command>
12 </xml> 12 </xml>
214 <xml name="gtf_options"> 214 <xml name="gtf_options">
215 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue="" 215 <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
216 label="Use a metagene model" 216 label="Use a metagene model"
217 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." /> 217 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
218 <param argument="--transcriptID" optional="True" value="transcript" type="text" 218 <param argument="--transcriptID" optional="True" value="transcript" type="text"
219 label="trascript designator" 219 label="transcript designator"
220 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" /> 220 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
221 <param argument="--exonID" optional="True" value="exon" type="text" 221 <param argument="--exonID" optional="True" value="exon" type="text"
222 label="exon designator" 222 label="exon designator"
223 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" /> 223 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
224 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text" 224 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
652 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True" 652 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
653 label="Image dpi" help=""/> 653 label="Image dpi" help=""/>
654 </xml> 654 </xml>
655 655
656 <xml name="output_image_file_format"> 656 <xml name="output_image_file_format">
657 <data format="png" name="outFileName" label="${tool.name} image"> 657 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
658 <change_format> 658 <change_format>
659 <when input="output.outFileFormat" value="pdf" format="pdf" /> 659 <when input="output.outFileFormat" value="pdf" format="pdf" />
660 <when input="output.outFileFormat" value="svg" format="svg" /> 660 <when input="output.outFileFormat" value="svg" format="svg" />
661 <when input="output.outFileFormat" value="eps" format="eps" /> 661 <when input="output.outFileFormat" value="eps" format="eps" />
662 <when input="output.outFileFormat" value="plotly" format="html" /> 662 <when input="output.outFileFormat" value="plotly" format="html" />
663 </change_format> 663 </change_format>
664 </data> 664 </data>
665 </xml> 665 </xml>
666 666
667 <xml name="output_image_file_format_not_nested"> 667 <xml name="output_image_file_format_not_nested">
668 <data format="png" name="outFileName" label="${tool.name} image"> 668 <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
669 <change_format> 669 <change_format>
670 <when input="outFileFormat" value="pdf" format="pdf" /> 670 <when input="outFileFormat" value="pdf" format="pdf" />
671 <when input="outFileFormat" value="svg" format="svg" /> 671 <when input="outFileFormat" value="svg" format="svg" />
672 <when input="outFileFormat" value="eps" format="eps" /> 672 <when input="outFileFormat" value="eps" format="eps" />
673 <when input="outFileFormat" value="plotly" format="html" /> 673 <when input="outFileFormat" value="plotly" format="html" />