Mercurial > repos > geert-vandeweyer > cuffquant
comparison cuffquant_wrapper.xml @ 1:e14baafb20bd draft
Added Test description, updated a few lines in the help
| author | geert-vandeweyer |
|---|---|
| date | Mon, 04 Aug 2014 10:43:34 -0400 |
| parents | 851fe29d1f20 |
| children |
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| 0:851fe29d1f20 | 1:e14baafb20bd |
|---|---|
| 46 --max-mle-iterations=$advanced_settings.max_mle_iterations | 46 --max-mle-iterations=$advanced_settings.max_mle_iterations |
| 47 --max-bundle-frags=$advanced_settings.max_bundle_frags | 47 --max-bundle-frags=$advanced_settings.max_bundle_frags |
| 48 #end if | 48 #end if |
| 49 ## Inputs. | 49 ## Inputs. |
| 50 $gtf_input | 50 $gtf_input |
| 51 #for $condition in $conditions: | 51 #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) |
| 52 #set samples = ','.join( [ str( $sample.sample ) for $sample in $condition.samples ] ) | 52 $samplestring |
| 53 $samples | |
| 54 #end for | |
| 55 </command> | 53 </command> |
| 56 <inputs> | 54 <inputs> |
| 57 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> | 55 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/> |
| 58 | 56 |
| 59 <repeat name="conditions" title="Condition" min="1"> | 57 <repeat name="samples" title="Replicate" min="1"> |
| 60 <param name="name" title="Condition name" type="text" label="Name"/> | 58 <param name="sample" label="Add replicate" type="data" format="sam,bam"/> |
| 61 <repeat name="samples" title="Replicate" min="1"> | 59 </repeat> |
| 62 <param name="sample" label="Add replicate" type="data" format="sam,bam"/> | |
| 63 </repeat> | |
| 64 </repeat> | |
| 65 | 60 |
| 66 | 61 |
| 67 <param name="multiread_correct" type="boolean" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." /> | 62 <param name="multiread_correct" type="boolean" label="Use multi-read correct" help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." /> |
| 68 | 63 |
| 69 <conditional name="bias_correction"> | 64 <conditional name="bias_correction"> |
| 128 <option value="fr-unstranded" >fr-unstranded</option> | 123 <option value="fr-unstranded" >fr-unstranded</option> |
| 129 <option value="transfrags">transfrags</option> | 124 <option value="transfrags">transfrags</option> |
| 130 </param> | 125 </param> |
| 131 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> | 126 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> |
| 132 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> | 127 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> |
| 133 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" /> | 128 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" help="Sets the maximum number of fragments a locus may have before being skipped. Default: 500,000" /> |
| 134 | 129 |
| 135 </when> | 130 </when> |
| 136 </conditional> | 131 </conditional> |
| 137 </inputs> | 132 </inputs> |
| 138 | 133 |
| 148 </outputs> | 143 </outputs> |
| 149 | 144 |
| 150 <tests> | 145 <tests> |
| 151 <test> | 146 <test> |
| 152 <!-- | 147 <!-- |
| 153 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam | 148 cuffquant cuffcompare_out5.gtf cuffdiff_in1.sam,cuffdiff_in2.sam |
| 154 --> | 149 --> |
| 155 <!-- | 150 <param name="gtf_input" value="cuffquant_in.gtf" ftype="gtf" /> |
| 156 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat | 151 <param name="sample1" value="cuffquant_in1.sam" ftype="sam" /> |
| 157 element are not supported. | 152 <param name="sample2" value="cuffquant_in2.sam" ftype="sam" /> |
| 158 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf" /> | 153 <param name="length_correction" value="cufflinks effective length correction" /> |
| 159 <param name="do_groups" value="No" /> | |
| 160 <param name="aligned_reads1" value="cuffdiff_in1.sam" ftype="sam" /> | |
| 161 <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" /> | |
| 162 <param name="fdr" value="0.05" /> | |
| 163 <param name="min_alignment_count" value="0" /> | |
| 164 <param name="do_bias_correction" value="No" /> | 154 <param name="do_bias_correction" value="No" /> |
| 165 <param name="do_normalization" value="No" /> | |
| 166 <param name="multiread_correct" value="No"/> | 155 <param name="multiread_correct" value="No"/> |
| 167 <param name="sAdditional" value="No"/> | 156 <param name="sAdditional" value="No"/> |
| 168 <output name="splicing_diff" file="cuffdiff_out9.txt"/> | 157 <param name="sAdvanced" value="No" /> |
| 169 <output name="promoters_diff" file="cuffdiff_out10.txt"/> | 158 <output name="out_file" file="cuffquant_out1.cxb"/> |
| 170 <output name="cds_diff" file="cuffdiff_out11.txt"/> | |
| 171 <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> | |
| 172 <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> | |
| 173 <output name="tss_groups_exp" file="cuffdiff_out3.txt" lines_diff="200"/> | |
| 174 <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> | |
| 175 <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> | |
| 176 <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> | |
| 177 <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> | |
| 178 <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/> | |
| 179 --> | |
| 180 </test> | 159 </test> |
| 181 </tests> | 160 </tests> |
| 182 | 161 |
| 183 <help> | 162 <help> |
| 184 **Cuffquant Overview** | 163 **Cuffquant Overview** |