cuffdiff: cuffdiff_wrapper.xml annotate

annotate cuffdiff_wrapper.xml @ 17:43221aef70e2 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 0e1d7660ab8ccb677b4f79207f5bc78097640f04"

author	iuc
date	Sat, 27 Nov 2021 09:58:11 +0000
parents	af3e173cad7f
children	a85acc5199c7

rev	line source
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	1 <tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.6">
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	2 <description>find significant changes in transcript expression, splicing, and promoter use</description>
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	3 <macros>
15 43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 14 diff changeset	4 <import>cuff_macros.xml</import>
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	5 </macros>
13 f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 12 diff changeset	6 <expand macro="requirements">
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	7 <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
13 f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 12 diff changeset	8 </expand>
15 43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 14 diff changeset	9 <version_command><![CDATA[cuffdiff 2>&1 \| head -n 1]]></version_command>
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	10 <command detect_errors="aggressive"><![CDATA[
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	11 cuffdiff
2 2d6a90609943 Fix wrapper bugs: (a) do not try update check and (b) allow spaces in labels. jeremy goecks <jeremy.goecks@emory.edu> parents: 1 diff changeset	12 --no-update-check
12 0f32ad418df8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit a1517c9d22029095120643bbe2c8fa53754dd2b7 devteam parents: 11 diff changeset	13 --quiet
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	14 --FDR=$fdr
6 604fa75232a2 Convert tool to use $GALAXY_SLOTS if available. Nate Coraor <nate@bx.psu.edu> parents: 3 diff changeset	15 --num-threads="\${GALAXY_SLOTS:-4}"
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	16 --min-alignment-count=$min_alignment_count
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	17 --library-norm-method=$library_norm_method
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	18 --dispersion-method=$dispersion_method
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	19
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	20 ## Set advanced SE data parameters?
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	21 #if $additional.sAdditional == "Yes":
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	22 -m $additional.frag_mean_len
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	23 -s $additional.frag_len_std_dev
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	24 #end if
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	25
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	26 ## Multi-read correct?
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	27 #if $multiread_correct :
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	28 -u
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	29 #end if
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	30
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	31 ## Bias correction?
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	32 #if $bias_correction.do_bias_correction == "Yes":
1 60a52f8460a1 Fix bias correction. jeremy goecks <jeremy.goecks@emory.edu> parents: 0 diff changeset	33 -b
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	34 #if $bias_correction.seq_source.index_source == "history":
1 60a52f8460a1 Fix bias correction. jeremy goecks <jeremy.goecks@emory.edu> parents: 0 diff changeset	35 ## Custom genome from history.
13 f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 12 diff changeset	36 '$bias_correction.seq_source.ref_file'
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	37 #else:
1 60a52f8460a1 Fix bias correction. jeremy goecks <jeremy.goecks@emory.edu> parents: 0 diff changeset	38 ## Built-in genome.
13 f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 12 diff changeset	39 '${bias_correction.seq_source.index.fields.path}'
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	40 #end if
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	41 #end if
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	42
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	43 @CONDITION_LABELS@
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	44
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	45 $length_correction
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	46
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	47 ## Set advanced parameters for cufflinks
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	48 #if $advanced_settings.sAdvanced == "Yes":
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	49 #if str($advanced_settings.library_type) != 'auto':
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	50 --library-type=$advanced_settings.library_type
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	51 #end if
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	52 #if $advanced_settings.mask_file:
13 f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 12 diff changeset	53 --mask-file '$advanced_settings.mask_file'
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	54 #end if
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	55 #if $advanced_settings.time_series:
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	56 --time-series
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	57 #end if
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	58 --max-mle-iterations=$advanced_settings.max_mle_iterations
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	59 $advanced_settings.hits_norm
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	60 --max-bundle-frags=$advanced_settings.max_bundle_frags
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	61 --num-frag-count-draws=$advanced_settings.num_frag_count_draws
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	62 --num-frag-assign-draws=$advanced_settings.num_frag_assign_draws
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	63 --min-reps-for-js-test=$advanced_settings.min_reps_for_js_test
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	64 #end if
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	65 ## Inputs.
13 f1b92120dfaa planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 12 diff changeset	66 '$gtf_input'
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	67
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	68 @CONDITION_SAMPLES@
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	69 #if $generate_sqlite:
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	70 &&
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	71 Rscript '$__tool_directory__/cummeRbund.R'
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	72 #end if
8 88fcac97c2a0 Uploaded updated cuffdiff. devteam parents: 7 diff changeset	73 ]]>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	74 </command>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	75 <inputs>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	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."/>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	77 <param name="omit_tabular_output" type="boolean" truevalue="yes" falsevalue="no" label="Omit Tabular Datasets" help="Discard the tabular output." />
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	78 <param name="generate_sqlite" type="boolean" truevalue="yes" falsevalue="no" label="Generate SQLite" help="Generate a SQLite database for use with cummeRbund." />
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	79 <expand macro="condition_inputs" />
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	80 <param name="library_norm_method" type="select" label="Library normalization method">
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	81 <option value="geometric" selected="True">geometric</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	82 <option value="classic-fpkm">classic-fpkm</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	83 <option value="quartile">quartile</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	84 </param>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	85
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	86 <param name="dispersion_method" type="select" label="Dispersion estimation method" help="If using only one sample per condition, you must use 'blind.'">
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	87 <option value="pooled" selected="True">pooled</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	88 <option value="per-condition">per-condition</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	89 <option value="blind">blind</option>
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	90 <option value="poisson">poisson</option>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	91 </param>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	92
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	93 <param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/>
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	94 <param name="min_alignment_count" type="integer" value="10" label="Min Alignment Count"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	95 help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/>
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	96 <param name="multiread_correct" type="boolean" label="Use multi-read correct"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	97 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome." />
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	98
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	99 <conditional name="bias_correction">
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	100 <param name="do_bias_correction" type="select" label="Perform Bias Correction"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	101 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	102 <option value="No">No</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	103 <option value="Yes">Yes</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	104 </param>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	105 <when value="Yes">
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	106 <conditional name="seq_source">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	107 <param name="index_source" type="select" label="Reference sequence data">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	108 <option value="cached">Locally cached</option>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	109 <option value="history">History</option>
3 beab768feb92 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 2 diff changeset	110 </param>
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	111 <when value="cached">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	112 <param name="index" type="select" label="Using reference genome">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	113 <options from_data_table="fasta_indexes">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	114 <filter type="data_meta" ref="gtf_input" key="dbkey" column="1" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	115 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	116 </options>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	117 </param>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	118 </when>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	119 <when value="history">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	120 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	121 </when>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	122 </conditional>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	123 </when>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	124 <when value="No"></when>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	125 </conditional>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	126
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	127 <param name="include_read_group_files" type="select" label="Include Read Group Datasets" help="Read group datasets provide information on replicates.">
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	128 <option value="No" selected="true">No</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	129 <option value="Yes">Yes</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	130 </param>
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	131
d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	132 <param name="include_count_files" type="select" label="Include Count Based output files"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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.">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	134 <option value="No" selected="true">No</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	135 <option value="Yes">Yes</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	136 </param>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	137
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	138 <param name="length_correction" type="select" label="apply length correction" help="mode of length normalization to transcript fpkm.">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	139 <option value="" selected="true">cufflinks effective length correction</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	140 <option value="--no-effective-length-correction">standard length correction</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	141 <option value="--no-length-correction">no length correction at all (use raw counts)</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	142 </param>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	143
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	144 <conditional name="additional">
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	145 <param name="sAdditional" type="select" label="Set Additional Parameters for single end reads? (not recommended for paired-end reads)">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	146 <option value="No" selected="True">No</option>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	147 <option value="Yes">Yes</option>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	148 </param>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	149 <when value="No"></when>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	150 <when value="Yes">
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	151 <param name="frag_mean_len" type="integer" value="200" label="Average Fragment Length"/>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	152 <param name="frag_len_std_dev" type="integer" value="80" label="Fragment Length Standard Deviation"/>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	153 </when>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	154 </conditional>
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	155
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	156 <conditional name="advanced_settings">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	157 <param name="sAdvanced" type="select" label="Set Advanced Cuffdiff parameters? ">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	158 <option value="No" selected="True">No</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	159 <option value="Yes">Yes</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	160 </param>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	161 <when value="No"></when>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	162 <when value="Yes">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	163 <param type="select" name="library_type" label="Library prep used for input reads" help="">
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	164 <option value="auto" selected="True">Auto Detect</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	165 <option value="ff-firststrand">ff-firststrand</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	166 <option value="ff-secondstrand">ff-secondstrand</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	167 <option value="ff-unstranded">ff-unstranded</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	168 <option value="fr-firststrand">fr-firststrand</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	169 <option value="fr-secondstrand">fr-secondstrand</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	170 <option value="fr-unstranded" >fr-unstranded</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	171 <option value="transfrags">transfrags</option>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	172 </param>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	173 <param name="mask_file" type="data" format="gtf,gff3" label="Mask File" help="Ignore all alignment within transcripts in this file" optional="True" />
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	174 <param name="time_series" type="boolean" label="Perform Time Series analysis"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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.)" />
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	176 <param name="max_mle_iterations" value="5000" type="integer" label="Max MLE iterations" help="Maximum iterations allowed for Maximal Likelyhood Estimation calculations" />
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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." >
15 43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 14 diff changeset	178 <option value="--compatible-hits-norm" selected="True">Compatible Hits</option>
43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 14 diff changeset	179 <option value="--total-hits-norm">All Hits</option>
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	180 </param>
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	181 <param name="max_bundle_frags" type="integer" value="500000" label="Maximum number of fragments per locus"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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" />
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	183 <param name="num_frag_count_draws" type="integer" value="100" label="Number of fragment generation samples"
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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."/>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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."/>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	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." />
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	187 </when>
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	188 </conditional>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	189 </inputs>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	190 <outputs>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	191 <!-- Optional read group datasets. -->
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	192 <data format="tabular" name="isoforms_read_group" label="${tool.name} on ${on_string}: isoforms read group tracking" from_work_dir="isoforms.read_group_tracking" >
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	193 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	194 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	195 <data format="tabular" name="genes_read_group" label="${tool.name} on ${on_string}: genes read group tracking" from_work_dir="genes.read_group_tracking" >
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	196 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	197 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	198 <data format="tabular" name="cds_read_group" label="${tool.name} on ${on_string}: CDs read group tracking" from_work_dir="cds.read_group_tracking" >
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	199 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	200 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	201 <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	202 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	203 </data>
11 5ce5197de50c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty devteam parents: 10 diff changeset	204 <data format="txt" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	205 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	206 </data>
11 5ce5197de50c planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty devteam parents: 10 diff changeset	207 <data format="txt" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	208 <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	209 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	210 <!-- Standard datasets. -->
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	211 <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing" from_work_dir="splicing.diff">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	212 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	213 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	214 <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing" from_work_dir="promoters.diff">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	215 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	216 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	217 <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing" from_work_dir="cds.diff">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	218 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	219 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	220 <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing" from_work_dir="cds_exp.diff">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	221 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	222 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	223 <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking" from_work_dir="cds.fpkm_tracking">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	224 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	225 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	226 <data format="tabular" name="cds_count_tracking" label="${tool.name} on ${on_string}: CDS count tracking" from_work_dir="cds.count_tracking" >
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	227 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	228 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	229
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	230 <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing" from_work_dir="tss_group_exp.diff">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	231 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	232 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	233 <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" from_work_dir="tss_groups.fpkm_tracking">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	234 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	235 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	236 <data format="tabular" name="tss_groups_count_tracking" label="${tool.name} on ${on_string}: TSS count FPKM tracking" from_work_dir="tss_groups.count_tracking" >
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	237 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	238 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	239
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	240 <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing" from_work_dir="gene_exp.diff">
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	241 <filter>not omit_tabular_output</filter>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	242 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	243 <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking" from_work_dir="genes.fpkm_tracking">
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	244 <filter>not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	245 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	246 <data format="tabular" name="genes_count_tracking" label="${tool.name} on ${on_string}: gene count tracking" from_work_dir="genes.count_tracking" >
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	247 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	248 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	249
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	250 <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing" from_work_dir="isoform_exp.diff">
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	251 <filter>not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	252 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	253 <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking" from_work_dir="isoforms.fpkm_tracking">
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	254 <filter>not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	255 </data>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	256 <data format="tabular" name="isoforms_count_tracking" label="${tool.name} on ${on_string}: transcript count tracking" from_work_dir="isoforms.count_tracking">
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	257 <filter>(include_count_files == 'Yes') and not omit_tabular_output</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	258 </data>
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	259 <data format="sqlite" name="output_cummerbund" label="${tool.name} on ${on_string}: cummeRbund SQLite database" from_work_dir="cummeRbund.sqlite">
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	260 <filter>generate_sqlite</filter>
4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	261 </data>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	262 </outputs>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	263
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	264 <tests>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	265 <test>
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	266 <!--
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	267 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	268 -->
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	269 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	270 <param name="generate_sqlite" value="yes" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	271 <param name="omit_tabular_output" value="yes" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	272 <conditional name="in_type">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	273 <param name="set_in_type" value="BAM" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	274 <repeat name="conditions">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	275 <param name="name" value="q1" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	276 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	277 </repeat>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	278 <repeat name="conditions">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	279 <param name="name" value="q2" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	280 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	281 </repeat>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	282 </conditional>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	283 <param name="fdr" value="0.05" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	284 <param name="min_alignment_count" value="0" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	285 <param name="do_bias_correction" value="No" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	286 <param name="multiread_correct" value="No"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	287 <param name="sAdditional" value="No"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	288 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	289 </test>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	290 <test>
16 af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	291 <!--
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	292 Use a list collection as conditions input
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	293 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	294 -->
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	295 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	296 <param name="generate_sqlite" value="yes" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	297 <param name="omit_tabular_output" value="yes" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	298 <conditional name="in_type">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	299 <param name="set_in_type" value="CONDITION_LIST" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	300 <param name="conditions">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	301 <collection type="list">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	302 <element name="q1" value="cuffdiff_in1.sam" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	303 <element name="q2" value="cuffdiff_in2.sam" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	304 </collection>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	305 </param>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	306 </conditional>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	307 <param name="fdr" value="0.05" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	308 <param name="min_alignment_count" value="0" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	309 <param name="do_bias_correction" value="No" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	310 <param name="multiread_correct" value="No"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	311 <param name="sAdditional" value="No"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	312 <output name="output_cummerbund" ftype="sqlite" file="cuffdiff_out.sqlite" compare="sim_size" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	313 </test>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	314 <test>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	315 <!--
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	316 cuffdiff cuffcompare_out5.gtf cuffdiff_in1.sam cuffdiff_in2.sam
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	317 -->
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	318 <param name="gtf_input" value="cuffdiff_in1.gtf" ftype="gtf" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	319 <param name="omit_tabular_output" value="no" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	320 <conditional name="in_type">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	321 <param name="set_in_type" value="BAM" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	322 <repeat name="conditions">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	323 <param name="name" value="q1" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	324 <param name="samples" value="cuffdiff_in1.sam" ftype="sam" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	325 </repeat>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	326 <repeat name="conditions">
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	327 <param name="name" value="q2" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	328 <param name="samples" value="cuffdiff_in2.sam" ftype="sam" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	329 </repeat>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	330 </conditional>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	331 <param name="fdr" value="0.05" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	332 <param name="min_alignment_count" value="0" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	333 <param name="do_bias_correction" value="No" />
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	334 <param name="multiread_correct" value="No"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	335 <param name="sAdditional" value="No"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	336 <output name="splicing_diff" file="splicing.diff"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	337 <output name="promoters_diff" file="promoters.diff"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	338 <output name="cds_diff" file="cds.diff"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	339 <output name="cds_exp_fpkm_tracking" file="cds.exp_fpkm_tracking"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	340 <output name="cds_fpkm_tracking" file="cds.fpkm_tracking"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	341 <output name="tss_groups_exp" file="tss.groups_exp" lines_diff="200"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	342 <output name="tss_groups_fpkm_tracking" file="tss.groups_fpkm_tracking"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	343 <output name="genes_exp" file="genes.exp" lines_diff="200"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	344 <output name="genes_fpkm_tracking" file="genes.fpkm_tracking" lines_diff="200"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	345 <output name="isoforms_exp" file="isoforms.exp" lines_diff="200"/>
af3e173cad7f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit 6b66cbbde16c35593fe95066ea2b91623bf35140" iuc parents: 15 diff changeset	346 <output name="isoforms_fpkm_tracking" file="isoforms.fpkm_tracking" lines_diff="200"/>
10 4e6f043995ff planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 4f5f0b9c6f52d17728d97452749b5dc887f7d46a devteam parents: 8 diff changeset	347 </test>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	348 </tests>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	349 <help>
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	350 Cuffdiff Overview
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	351
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	352 Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	353
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	354 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	355
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	356 ------
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	357
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	358 Know what you are doing
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	359
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	360 .. class:: warningmark
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	361
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	362 There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to understand the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	363
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	364 .. __: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	365
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	366 ------
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	367
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	368 Input format
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	369
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	370 Cuffdiff takes Cufflinks or Cuffcompare GTF files as input along with two SAM files containing the fragment alignments for two or more samples.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	371
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	372 ------
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	373
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	374 Outputs
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	375
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	376 Cuffdiff produces many output files:
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	377
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	378 1. Transcript FPKM (+count) expression tracking.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	379 2. Gene FPKM (+count) expression tracking; tracks the summed FPKM of transcripts sharing each gene_id
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	380 3. Primary transcript FPKM (+count) tracking; tracks the summed FPKM of transcripts sharing each tss_id
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	381 4. Coding sequence FPKM (+count) tracking; tracks the summed FPKM of transcripts sharing each p_id, independent of tss_id
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	382 5. Transcript differential FPKM.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	383 6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	384 7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	385 8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	386 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.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	387 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.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	388 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.
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	389
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	390 -------
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	391
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	392 Settings
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	393
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	394 All of the options have a default value. You can change any of them. Most of the options in Cuffdiff have been implemented here.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	395
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	396 ------
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	397
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	398 Cuffdiff parameter list
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	399
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	400 This is a list of implemented Cuffdiff options::
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	401
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	402 -m INT Average fragment length (SE reads); default 200
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	403 -s INT Fragment legnth standard deviation (SE reads); default 80
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	404 -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	405 --FDR FLOAT The allowed false discovery rate. The default is 0.05.
0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	406 --max-mle-iterations INT Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	407 --library-norm-method Library Normalization method : Geometric (default), classic-fpkm, quartile
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	408 --dispersion-method Dispersion estimation method : Pooled (default), per-condition, blind, poisson
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	409 -u Multi read correction tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	410 -b ref.fasta bias correction. Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	411 --no-effective-length-correction Use standard length correction
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	412 --no-length-correction Disable all length correction.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	413 --library-type ff-firststrand,ff-secondstrand,ff-unstranded,fr-firstrand,fr-secondstrand,fr-unstranded,transfrags
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	414 --mask-file (gff3/gtf) Ignore all alignment within transcripts in this file
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	415 --time-series Treat provided sam files as time series
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	416 --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.
14 d3ae7d9c2202 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5 devteam parents: 13 diff changeset	417 --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
7 8da0eade1f59 Uploaded devteam parents: 6 diff changeset	418 --max-bundle-frags Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	419 --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.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	420 --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.
8da0eade1f59 Uploaded devteam parents: 6 diff changeset	421 --min-reps-for-js-test Cuffdiff won't test genes for differential regulation unless the conditions in question have at least this many replicates.
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	422 </help>
15 43b36b3d4333 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffdiff commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 14 diff changeset	423 <expand macro="citations"/>
0 0dabb2ed6eb1 Uploaded tool tarball. devteam parents: diff changeset	424 </tool>

Mercurial > repos > devteam > cuffdiff

annotate cuffdiff_wrapper.xml @ 17:43221aef70e2 draft