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comparison cuffquant_wrapper.xml @ 2:6c7e4034e354 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:06:19 -0500
parents 8fb10700729b
children 25cf1ab351df
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1:8fb10700729b 2:6c7e4034e354
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.