Mercurial > repos > devteam > cuffnorm
comparison cuffnorm_wrapper.xml @ 2:f8fdf50e0b3b draft
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 |
comparison
equal
deleted
inserted
replaced
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>&1 | head -n 1</version_command> | 8 <version_command>cuffnorm 2>&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 |