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comparison cuffnorm_wrapper.xml @ 2:f8fdf50e0b3b draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffnorm commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author devteam
date Tue, 07 Feb 2017 18:40:18 -0500
parents 7d4c2097aac5
children f5b2ee725d34
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1:7d4c2097aac5 2:f8fdf50e0b3b
1 <tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.1"> 1 <tool id="cuffnorm" name="Cuffnorm" version="@VERSION@.1">
2 <description>Create normalized expression levels</description> 2 <description>Create normalized expression levels</description>
3 <expand macro="requirements" />
4 <expand macro="stdio" />
5 <macros> 3 <macros>
6 <import>cuff_macros.xml</import> 4 <import>cuff_macros.xml</import>
7 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command> 8 <version_command>cuffnorm 2>&amp;1 | head -n 1</version_command>
9 <command> 9 <command>
10 cuffnorm 10 cuffnorm
11 --no-update-check 11 --no-update-check
12 --num-threads="\${GALAXY_SLOTS:-4}" 12 --num-threads="\${GALAXY_SLOTS:-4}"
40 help="Read group/attribute datasets provide information on replicates. One of both is provided, depending on the output format."> 40 help="Read group/attribute datasets provide information on replicates. One of both is provided, depending on the output format.">
41 <option value="No" selected="true">No</option> 41 <option value="No" selected="true">No</option>
42 <option value="Yes">Yes</option> 42 <option value="Yes">Yes</option>
43 </param> 43 </param>
44 44
45 <param name="output_format" type="select" lable="Output format" 45 <param name="output_format" type="select" label="Output format"
46 help="By default, Cuffnorm reports expression levels in the 'simple-table' tab-delimted text files. The program also reports information about your samples and about the genes, transcripts, TSS groups, and CDS groups as tab delimited text files. Note that these files have a different format than the files used by Cuffdiff. However, you can direct Cuffnorm to report its output in the same format as used by Cuffdiff if you wish" > 46 help="By default, Cuffnorm reports expression levels in the 'simple-table' tab-delimted text files. The program also reports information about your samples and about the genes, transcripts, TSS groups, and CDS groups as tab delimited text files. Note that these files have a different format than the files used by Cuffdiff. However, you can direct Cuffnorm to report its output in the same format as used by Cuffdiff if you wish" >
47 <option value="simple-table" selected="True">Simple Table</option> 47 <option value="simple-table" selected="True">Simple Table</option>
48 <option value="cuffdiff">Cuffdiff format</option> 48 <option value="cuffdiff">Cuffdiff format</option>
49 </param> 49 </param>
50 50
164 <data format="tabular" name="isoforms_count_table" label="${tool.name} on ${on_string}: transcript count table" from_work_dir="isoforms.count_table" > 164 <data format="tabular" name="isoforms_count_table" label="${tool.name} on ${on_string}: transcript count table" from_work_dir="isoforms.count_table" >
165 <filter>(output_format == 'simple-table')</filter> 165 <filter>(output_format == 'simple-table')</filter>
166 </data> 166 </data>
167 </outputs> 167 </outputs>
168 <tests> 168 <tests>
169 <!--
169 <test> 170 <test>
170 <!--
171 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat 171 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat
172 element are not supported. 172 element are not supported.
173 -->
174 </test> 173 </test>
174 -->
175 </tests> 175 </tests>
176 176
177 <help> 177 <help>
178 **Cuffnorm Overview** 178 **Cuffnorm Overview**
179 179