Mercurial > repos > devteam > cuffdiff

comparison cuffdiff_wrapper.xml @ 14:d3ae7d9c2202 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5
author devteam
date Sun, 19 Feb 2017 12:12:17 -0500
parents f1b92120dfaa
children 43b36b3d4333
comparison
equal deleted inserted replaced
13:f1b92120dfaa 14:d3ae7d9c2202
1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.4"> 1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.5">
2 <description>find significant changes in transcript expression, splicing, and promoter use</description> 2 <description>find significant changes in transcript expression, splicing, and promoter use</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 <requirement type="package" version="2.8.2">bioconductor-cummerbund</requirement> 7 <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
8 </expand> 8 </expand>
9 <expand macro="stdio" />
10 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command> 9 <version_command>cuffdiff 2>&amp;1 | head -n 1</version_command>
11 <command><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
12 cuffdiff 11 cuffdiff
13 --no-update-check 12 --no-update-check
14 --quiet 13 --quiet
15 --FDR=$fdr 14 --FDR=$fdr
16 --num-threads="\${GALAXY_SLOTS:-4}" 15 --num-threads="\${GALAXY_SLOTS:-4}"
67 '$gtf_input' 66 '$gtf_input'
68 67
69 @CONDITION_SAMPLES@ 68 @CONDITION_SAMPLES@
70 #if $generate_sqlite: 69 #if $generate_sqlite:
71 && 70 &&
72 R --vanilla --no-save -f '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}' 71 Rscript '$__tool_directory__/cummeRbund.R' && mv cummeRbund.sqlite '${output_cummerbund}'
73 #end if 72 #end if
74 ]]> 73 ]]>
75 </command> 74 </command>
76 <inputs> 75 <inputs>
77 <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."/> 76 <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."/>
90 <option value="blind">blind</option> 89 <option value="blind">blind</option>
91 <option value="poisson">poisson</option> 90 <option value="poisson">poisson</option>
92 </param> 91 </param>
93 92
94 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> 93 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
95 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count" 94 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count"
96 help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/> 95 help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
97 <param name="multiread_correct" type="boolean" label="Use multi-read correct" 96 <param name="multiread_correct" type="boolean" label="Use multi-read correct"
98 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." /> 97 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." />
99 98
100 <conditional name="bias_correction"> 99 <conditional name="bias_correction">
101 <param name="do_bias_correction" type="select" label="Perform Bias Correction" 100 <param name="do_bias_correction" type="select" label="Perform Bias Correction"
102 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates."> 101 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
103 <option value="No">No</option> 102 <option value="No">No</option>
104 <option value="Yes">Yes</option> 103 <option value="Yes">Yes</option>
105 </param> 104 </param>
106 <when value="Yes"> 105 <when value="Yes">
127 126
128 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates."> 127 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
129 <option value="No" selected="true">No</option> 128 <option value="No" selected="true">No</option>
130 <option value="Yes">Yes</option> 129 <option value="Yes">Yes</option>
131 </param> 130 </param>
132 131
133 <param name="include_count_files" type="select" label="Include Count Based output files" 132 <param name="include_count_files" type="select" label="Include Count Based output files"
134 help="Cuffdiff estimates the number of fragments that originated from each transcript, primary transcript, and gene in each sample. Primary transcript and gene counts are computed by summing the counts of transcripts in each primary transcript group or gene group."> 133 help="Cuffdiff estimates the number of fragments that originated from each transcript, primary transcript, and gene in each sample. Primary transcript and gene counts are computed by summing the counts of transcripts in each primary transcript group or gene group.">
135 <option value="No" selected="true">No</option> 134 <option value="No" selected="true">No</option>
136 <option value="Yes">Yes</option> 135 <option value="Yes">Yes</option>
137 </param> 136 </param>
138 137
170 <option value="fr-secondstrand">fr-secondstrand</option> 169 <option value="fr-secondstrand">fr-secondstrand</option>
171 <option value="fr-unstranded" >fr-unstranded</option> 170 <option value="fr-unstranded" >fr-unstranded</option>
172 <option value="transfrags">transfrags</option> 171 <option value="transfrags">transfrags</option>
173 </param> 172 </param>
174 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" /> 173 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
175 <param name="time_series" type="boolean" label="Perform Time Series analysis" 174 <param name="time_series" type="boolean" label="Perform Time Series analysis"
176 help="Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)" /> 175 help="Instructs Cuffdiff to analyze the provided samples as a time series, rather than testing for differences between all pairs of samples. Samples should be provided in increasing time order at the command line (e.g first time point SAM, second timepoint SAM, etc.)" />
177 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" /> 176 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
178 <param name="hits_norm" type="select" label="Hits included in normalization" help="All Hits: 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. Compatible Hits: 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. It is active by default." > 177 <param name="hits_norm" type="select" label="Hits included in normalization" help="All Hits: 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. Compatible Hits: 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. It is active by default." >
179 <option value="--compatible-hits-norm" selected="True">Compatible Hits</option> 178 <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
180 <option value="--total-hits-norm">All Hits</option> 179 <option value="--total-hits-norm">All Hits</option>
181 </param> 180 </param>
182 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus" 181 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
183 help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" /> 182 help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 500,000" />
184 <param name="num_frag_count_draws" type="integer" value="100" label="Number of fragment generation samples" 183 <param name="num_frag_count_draws" type="integer" value="100" label="Number of fragment generation samples"
185 help="Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 100."/> 184 help="Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 100."/>
186 <param name="num_frag_assign_draws" type="integer" value="50" label="Number of fragment assignment samples per generation" help="For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 50."/> 185 <param name="num_frag_assign_draws" type="integer" value="50" label="Number of fragment assignment samples per generation" help="For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. Default: 50."/>
187 <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." /> 186 <param name="min_reps_for_js_test" type="integer" value="3" label="Minimal Replicates for isoform shift testing" help="Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. Default: 3." />
188 </when> 187 </when>
189 </conditional> 188 </conditional>
263 </outputs> 262 </outputs>
264 263
265 <tests> 264 <tests>
266 <test> 265 <test>
267 <!-- 266 <!--
268 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 267 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
269 --> 268 -->
270 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> 269 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
271 <param name="generate_sqlite" value="yes" /> 270 <param name="generate_sqlite" value="yes" />
272 <param name="omit_tabular_output" value="yes" /> 271 <param name="omit_tabular_output" value="yes" />
273 <conditional name="in_type"> 272 <conditional name="in_type">
289 <param name="sAdditional" value="No"/> 288 <param name="sAdditional" value="No"/>
290 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" /> 289 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
291 </test> 290 </test>
292 <test> 291 <test>
293 <!-- 292 <!--
294 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam 293 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
295 --> 294 -->
296 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" /> 295 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
297 <param name="omit_tabular_output" value="no" /> 296 <param name="omit_tabular_output" value="no" />
298 <conditional name="in_type"> 297 <conditional name="in_type">
299 <param name="set_in_type" value="BAM" /> 298 <param name="set_in_type" value="BAM" />
363 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id 362 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id
364 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id 363 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id
365 9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file. 364 9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file.
366 10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here. 365 10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here.
367 11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here. 366 11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here.
368 367
369 ------- 368 -------
370 369
371 **Settings** 370 **Settings**
372 371
373 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here. 372 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
391 --no-length-correction Disable all length correction. 390 --no-length-correction Disable all length correction.
392 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags 391 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
393 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file 392 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file
394 --time-series Treat provided sam files as time series 393 --time-series Treat provided sam files as time series
395 --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. 394 --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.
396 --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 395 --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
397 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. 396 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
398 --num-frag-count-draws Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts. 397 --num-frag-count-draws Cuffdiff will make this many draws from each transcript's predicted negative binomial random numbder generator. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome. Used to estimate the variance-covariance matrix on assigned fragment counts.
399 --num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts. 398 --num-frag-assign-draws For each fragment drawn from a transcript, Cuffdiff will assign it this many times (probabilistically), thus estimating the assignment uncertainty for each transcript. Used to estimate the variance-covariance matrix on assigned fragment counts.
400 --min-reps-for-js-test Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates. 399 --min-reps-for-js-test Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates.
401 </help> 400 </help>