Mercurial > repos > devteam > cuffnorm
comparison cuffnorm_wrapper.xml @ 4:6cbfede05833 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffnorm commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author | iuc |
---|---|
date | Tue, 16 Jun 2020 13:01:30 -0400 |
parents | f5b2ee725d34 |
children | 9a854107dbb2 |
comparison
equal
deleted
inserted
replaced
3:f5b2ee725d34 | 4:6cbfede05833 |
---|---|
2 <description>Create normalized expression levels</description> | 2 <description>Create normalized expression levels</description> |
3 <macros> | 3 <macros> |
4 <import>cuff_macros.xml</import> | 4 <import>cuff_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <version_command>cuffnorm 2>&1 | head -n 1</version_command> | 7 <version_command><![CDATA[cuffnorm 2>&1 | head -n 1]]></version_command> |
8 <command detect_errors="aggressive"> | 8 <command detect_errors="aggressive"><![CDATA[ |
9 cuffnorm | 9 cuffnorm |
10 --no-update-check | 10 --no-update-check |
11 --num-threads="\${GALAXY_SLOTS:-4}" | 11 --num-threads="\${GALAXY_SLOTS:-4}" |
12 --library-norm-method=$library_norm_method | 12 --library-norm-method=$library_norm_method |
13 --output-format=$output_format | 13 --output-format=$output_format |
20 --library-type=$advanced_settings.library_type | 20 --library-type=$advanced_settings.library_type |
21 #end if | 21 #end if |
22 $advanced_settings.hits_norm | 22 $advanced_settings.hits_norm |
23 #end if | 23 #end if |
24 ## Inputs. | 24 ## Inputs. |
25 $gtf_input | 25 '$gtf_input' |
26 | 26 |
27 @CONDITION_SAMPLES@ | 27 @CONDITION_SAMPLES@ |
28 </command> | 28 ]]></command> |
29 <inputs> | 29 <inputs> |
30 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/> | 30 <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/> |
31 <expand macro="condition_inputs" /> | 31 <expand macro="condition_inputs" /> |
32 <param name="library_norm_method" type="select" label="Library normalization method"> | 32 <param name="library_norm_method" type="select" label="Library normalization method"> |
33 <option value="geometric" selected="True">geometric</option> | 33 <option value="geometric" selected="True">geometric</option> |
163 <data format="tabular" name="isoforms_count_table" label="${tool.name} on ${on_string}: transcript count table" from_work_dir="isoforms.count_table" > | 163 <data format="tabular" name="isoforms_count_table" label="${tool.name} on ${on_string}: transcript count table" from_work_dir="isoforms.count_table" > |
164 <filter>(output_format == 'simple-table')</filter> | 164 <filter>(output_format == 'simple-table')</filter> |
165 </data> | 165 </data> |
166 </outputs> | 166 </outputs> |
167 <tests> | 167 <tests> |
168 <!-- | 168 <test expect_num_outputs="8"> |
169 <test> | 169 <param name="gtf_input" value="cuffcompare_out5.gtf" ftype="gtf"/> |
170 NOTE: as of version 0.0.6 of the wrapper, tests cannot be run because multiple inputs to a repeat | 170 <conditional name="in_type"> |
171 element are not supported. | 171 <param name="set_in_type" value="BAM"/> |
172 <repeat name="conditions"> | |
173 <param name="name" value="in1"/> | |
174 <param name="samples" value="cuffdiff_in1.sam" ftype="sam"/> | |
175 </repeat> | |
176 <repeat name="conditions"> | |
177 <param name="name" value="in2"/> | |
178 <param name="samples" value="cuffdiff_in2.sam" ftype="sam"/> | |
179 </repeat> | |
180 </conditional> | |
181 <output ftype="tabular" name="cds_fpkm_table" value="cds.fpkm_table"/> | |
182 <output ftype="tabular" name="cds_count_table" value="cds.count_table"/> | |
183 <output ftype="tabular" name="tss_groups_fpkm_table" value="tss_groups.fpkm_table"/> | |
184 <output ftype="tabular" name="tss_groups_count_table" value="tss_groups.count_table"/> | |
185 <output ftype="tabular" name="genes_fpkm_table" value="genes.fpkm_table"/> | |
186 <output ftype="tabular" name="genes_count_table" value="genes.count_table"/> | |
187 <output ftype="tabular" name="isoforms_fpkm_table" value="isoforms.fpkm_table"/> | |
188 <output ftype="tabular" name="isoforms_count_table" value="isoforms.count_table"/> | |
172 </test> | 189 </test> |
173 --> | |
174 </tests> | 190 </tests> |
175 | 191 |
176 <help> | 192 <help> |
177 **Cuffnorm Overview** | 193 **Cuffnorm Overview** |
178 | 194 |
220 --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile | 236 --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile |
221 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags | 237 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags |
222 --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. | 238 --compatible-hits-norm With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped fragments used in the FPKM denominator. Using this mode is generally recommended in Cuffdiff to reduce certain types of bias caused by differential amounts of ribosomal reads which can create the impression of falsely differentially expressed genes. |
223 --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator | 239 --total-hits-norm With this option, Cufflinks counts all fragments, including those not compatible with any reference transcript, towards the number of mapped fragments used in the FPKM denominator |
224 </help> | 240 </help> |
225 <citations> | 241 <expand macro="citations"/> |
226 <citation type="doi">10.1038/nbt.1621</citation> | |
227 </citations> | |
228 </tool> | 242 </tool> |