Mercurial > repos > devteam > cuffquant
comparison cuffquant_wrapper.xml @ 1:986b63735a5e draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:35:31 -0500 |
| parents | 5d8b9dcaf17d |
| children | b2ee2bef1926 |
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| 0:5d8b9dcaf17d | 1:986b63735a5e |
|---|---|
| 126 <option value="fr-unstranded" >fr-unstranded</option> | 126 <option value="fr-unstranded" >fr-unstranded</option> |
| 127 <option value="transfrags">transfrags</option> | 127 <option value="transfrags">transfrags</option> |
| 128 </param> | 128 </param> |
| 129 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> | 129 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> |
| 130 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> | 130 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> |
| 131 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" | 131 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" |
| 132 help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" /> | 132 help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" /> |
| 133 </when> | 133 </when> |
| 134 </conditional> | 134 </conditional> |
| 135 </inputs> | 135 </inputs> |
| 136 <outputs> | 136 <outputs> |
| 138 <data format="cxb" name="out_file" label="${tool.name} on ${on_string}: Abundances.cxb" from_work_dir="abundances.cxb" /> | 138 <data format="cxb" name="out_file" label="${tool.name} on ${on_string}: Abundances.cxb" from_work_dir="abundances.cxb" /> |
| 139 </outputs> | 139 </outputs> |
| 140 <tests> | 140 <tests> |
| 141 <test> | 141 <test> |
| 142 <!-- | 142 <!-- |
| 143 cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam | 143 cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam |
| 144 --> | 144 --> |
| 145 <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" /> | 145 <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" /> |
| 146 <repeat name="samples"> | 146 <repeat name="samples"> |
| 147 <param name="sample" value="cuffquant_in1.sam" ftype="sam" /> | 147 <param name="sample" value="cuffquant_in1.sam" ftype="sam" /> |
| 148 </repeat> | 148 </repeat> |
| 186 **Outputs** | 186 **Outputs** |
| 187 | 187 |
| 188 Cuffquant produces one output file: | 188 Cuffquant produces one output file: |
| 189 | 189 |
| 190 1. Transcript expression values in binary format. | 190 1. Transcript expression values in binary format. |
| 191 | 191 |
| 192 ------- | 192 ------- |
| 193 | 193 |
| 194 **Settings** | 194 **Settings** |
| 195 | 195 |
| 196 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. | 196 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. |