cufflinks: cufflinks_wrapper.xml annotate

annotate cufflinks_wrapper.xml @ 12:d080005cffe1 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"

author	iuc
date	Tue, 16 Jun 2020 13:00:32 -0400
parents	e04dbae2abe0
children

rev	line source
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	1 <tool id="cufflinks" name="Cufflinks" version="@VERSION@.3">
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	2 <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	3 <macros>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	4 <import>cuff_macros.xml</import>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	5 </macros>
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	6 <expand macro="requirements">
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	7 <requirement type="package" version="3.6">python</requirement>
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	8 </expand>
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	9 <version_command><![CDATA[cufflinks 2>&1 \| head -n 1]]></version_command>
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	10 <command detect_errors="aggressive"><![CDATA[
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	11 cufflinks -q --no-update-check
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	12 '$input'
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	13 --num-threads "\${GALAXY_SLOTS:-4}"
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	14 -I $max_intron_len
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	15 -F $min_isoform_fraction
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	16 -j $pre_mrna_fraction
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	17 $length_correction
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	18
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	19 ## Include reference annotation?
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	20 #if $reference_annotation.use_ref == "Use reference annotation":
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	21 -G '$reference_annotation.reference_annotation_file'
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	22 $reference_annotation.compatible_hits_norm
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	23 #end if
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	24 #if $reference_annotation.use_ref == "Use reference annotation guide":
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	25 -g '$reference_annotation.reference_annotation_guide_file'
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	26 --3-overhang-tolerance $reference_annotation.three_overhang_tolerance
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	27 --intron-overhang-tolerance $reference_annotation.intron_overhang_tolerance
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	28 $reference_annotation.no_faux_reads
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	29 #end if
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	30
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	31 ## Bias correction?
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	32 #if $bias_correction.do_bias_correction == "Yes":
2 da11bfc10e81 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 0 diff changeset	33 -b
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	34 #if $bias_correction.seq_source.index_source == "history":
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	35 '$bias_correction.seq_source.ref_file'
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	36 #else:
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	37 '${bias_correction.seq_source.index.fields.path}'
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	38 #end if
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	39 #end if
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	40
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	41 ## Multi-read correct?
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	42 $multiread_correct
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	43
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	44 ## advanced settings
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	45 #if $advanced_settings.use_advanced_settings == "Yes":
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	46 --library-type $advanced_settings.library_type
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	47 #if $advanced_settings.mask_file:
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	48 --mask-file '$advanced_settings.mask_file'
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	49 #end if
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	50 --frag-len-mean $advanced_settings.inner_mean_dist
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	51 --frag-len-std-dev $advanced_settings.inner_dist_std_dev
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	52 --max-mle-iterations $advanced_settings.max_mle_iterations
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	53 --junc-alpha $advanced_settings.junc_alpha
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	54 --small-anchor-fraction $advanced_settings.small_anchor_fraction
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	55 --overhang-tolerance $advanced_settings.overhang_tolerance
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	56 --max-bundle-length $advanced_settings.max_bundle_length
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	57 --max-bundle-frags $advanced_settings.max_bundle_frags
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	58 --min-intron-length $advanced_settings.min_intron_length
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	59 --trim-3-avgcov-thresh $advanced_settings.trim_three_avgcov_thresh
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	60 --trim-3-dropoff-frac $advanced_settings.trim_three_dropoff_frac
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	61 #end if
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	62 2> stderr
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	63
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	64 && python '$__tool_directory__/mass.py' stderr '$global_model' "transcripts.gtf"
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	65 ]]></command>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	66 <inputs>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	67 <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	68 <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help="ignore alignments with gaps longer than this"/>
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	69 <param name="min_isoform_fraction" type="float" value="0.10" min="0" max="1" label="Min Isoform Fraction" help="suppress transcripts below this abundance level"/>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	70 <param name="pre_mrna_fraction" type="float" value="0.15" min="0" max="1" label="Pre MRNA Fraction" help="suppress intra-intronic transcripts below this level"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	71 <conditional name="reference_annotation">
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	72 <param name="use_ref" type="select" label="Use Reference Annotation">
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	73 <option value="No" selected="true">No</option>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	74 <option value="Use reference annotation">Use reference annotation</option>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	75 <option value="Use reference annotation guide">Use reference annotation as guide</option>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	76 </param>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	77 <when value="No" />
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	78 <when value="Use reference annotation">
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	79 <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	80 <param name="compatible_hits_norm" type="select" label="Count hits compatible with reference RNAs only"
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	81 help="With this option, Cufflinks counts only those fragments compatible with some reference transcript towards the number of mapped hits used in the FPKM denominator. This option can only be used in combination with --GTF.">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	82 <option value="" selected="True">No</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	83 <option value="--compatible-hits-norm">Yes</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	84 </param>
2 da11bfc10e81 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 0 diff changeset	85 </when>
da11bfc10e81 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 0 diff changeset	86 <when value="Use reference annotation guide">
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	87 <param format="gff3,gtf" name="reference_annotation_guide_file" type="data" label="Reference Annotation" help="Gene annotation dataset in GTF or GFF3 format."/>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	88 <param name="three_overhang_tolerance" type="integer" value="600" label="3prime overhang tolerance"
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	89 help="The number of bp allowed to overhang the 3prime end of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 600 bp." />
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	90 <param name="intron_overhang_tolerance" type="integer" value="50" label="Intronic overhang tolerance" help="The number of bp allowed to enter the intron of a reference transcript when determining if an assembled transcript should be merged with it (ie, the assembled transcript is not novel). The default is 50 bp." />
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	91 <param name="no_faux_reads" type="select" label="Disable tiling of reference transcripts" help="This option disables tiling of the reference transcripts with faux reads. Use this if you only want to use sequencing reads in assembly but do not want to output assembled transcripts that lay within reference transcripts. All reference transcripts in the input annotation will also be included in the output.">
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	92 <option value="" selected="True">No</option>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	93 <option value="--no-faux-reads">Yes</option>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	94 </param>
2 da11bfc10e81 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 0 diff changeset	95 </when>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	96 </conditional>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	97 <conditional name="bias_correction">
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	98 <param name="do_bias_correction" type="select" label="Perform Bias Correction"
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	99 help="Bias detection and correction can significantly improve accuracy of transcript abundance estimates.">
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	100 <option value="No" selected="true">No</option>
2 da11bfc10e81 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 0 diff changeset	101 <option value="Yes">Yes</option>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	102 </param>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	103 <when value="Yes">
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	104 <conditional name="seq_source">
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	105 <param name="index_source" type="select" label="Reference sequence data">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	106 <option value="cached" selected="true">Locally cached</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	107 <option value="history">History</option>
2 da11bfc10e81 Update to the new data table specification. Dave Bouvier <dave@bx.psu.edu> parents: 0 diff changeset	108 </param>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	109 <when value="cached">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	110 <param name="index" type="select" label="Using reference genome">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	111 <options from_data_table="fasta_indexes">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	112 <filter type="data_meta" ref="input" key="dbkey" column="1" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	113 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	114 </options>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	115 </param>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	116 </when>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	117 <when value="history">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	118 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	119 </when>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	120 </conditional>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	121 </when>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	122 <when value="No" />
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	123 </conditional>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	124
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	125 <param name="multiread_correct" type="boolean" label="Use multi-read correct"
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	126 truevalue="-u" falsevalue="" checked="false"
d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	127 help="Tells Cufflinks to do an initial estimation procedure to more accurately weight reads mapping to multiple locations in the genome."/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	128
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	129 <param name="length_correction" type="select" label="Apply length correction" help="Mode of length normalization to transcript FPKM.">
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	130 <option value="" selected="true">Cufflinks Effective Length Correction</option>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	131 <option value="--no-effective-length-correction">Standard Length Correction</option>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	132 <option value="--no-length-correction">No Length Correction at all (use raw counts)</option>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	133 </param>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	134
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	135 <param name="global_model" type="hidden_data" label="Global model (for use in Trackster)" optional="True"/>
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	136
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	137 <!-- advanced settings -->
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	138 <conditional name="advanced_settings">
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	139 <param name="use_advanced_settings" type="select" label="Set advanced Cufflinks options" help="">
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	140 <option value="No" selected="true">No</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	141 <option value="Yes" >Yes</option>
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	142 </param>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	143 <when value="No" />
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	144 <when value="Yes">
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	145 <param type="select" name="library_type" label="Library prep used for input reads" help="">
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	146 <option value="auto" selected="True">Auto Detect</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	147 <option value="ff-firststrand">ff-firststrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	148 <option value="ff-secondstrand">ff-secondstrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	149 <option value="ff-unstranded">ff-unstranded</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	150 <option value="fr-firststrand">fr-firststrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	151 <option value="fr-secondstrand">fr-secondstrand</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	152 <option value="fr-unstranded" >fr-unstranded</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	153 <option value="transfrags">transfrags</option>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	154 </param>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	155 <param name="mask_file" type="data" format="gff3,gtf" label="Mask File" help="Ignore all alignment within transcripts in this file " optional="True" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	156 <param name="inner_mean_dist" type="integer" value="45" label="Inner mean distance" help="This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp,where each end is 50bp, you should set it as 200. The default is 45bp." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	157 <param name="inner_dist_std_dev" type="integer" value="20" label="Inner distance standard deviation" help="The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	158 <param name="max_mle_iterations" type="integer" value="5000" label="Max MLE iterations" help="Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	159 <param name="junc_alpha" type="float" value="0.001" min="0" max="1" label="Alpha value for the binomial test used during false positive spliced alignment filtration" help="Default: 0.001" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	160 <param name="small_anchor_fraction" type="float" value="0.09" min="0" max="1" label="percent read overhang taken as suspiciously small" help="Spliced reads with less than this percent of their length on each side of the junction are considered suspicious and are candidates for filtering prior to assembly. Default: 0.09." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	161 <param name="overhang_tolerance" type="integer" value="8" label="Intronic overhang tolerance" help="The number of bp allowed to enter the intron of a transcript when determining if a read or another transcript is mappable to/compatible with it. The default is 8 bp based on the default bowtie/TopHat parameters." />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	162 <param name="max_bundle_length" type="integer" value="3500000" label="Maximum genomic length of a given bundle" help="Default: 3,500,000bp" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	163 <param name="max_bundle_frags" type="integer" value="1000000" label="Maximum number of fragments per locus" help="Sets the maximum number of fragments a locus may have before being skipped. Skipped loci are listed in skipped.gtf. Default: 1,000,000" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	164 <param name="min_intron_length" type="integer" value="50" label="Minimal allowed intron size" help="Default: 50bp" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	165 <param name="trim_three_avgcov_thresh" type="integer" value="10" label="Minimum average coverage required to attempt 3prime trimming." help="Default: 10" />
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	166 <param name="trim_three_dropoff_frac" type="float" value="0.1" min="0" max="1" label="The fraction of average coverage below which to trim the 3prime end of an assembled transcript." help="Default: 0.1"/>
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	167 </when>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	168 </conditional>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	169 </inputs>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	170 <outputs>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	171 <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	172 <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/>
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	173 <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts" from_work_dir="transcripts.gtf"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	174 <data format="txt" name="total_map_mass" label="${tool.name} on ${on_string}: total map mass" hidden="true" from_work_dir="global_model.txt"/>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	175 <data format="gtf" name="skipped" label="${tool.name} on ${on_string}: Skipped Transcripts" from_work_dir="skipped.gtf"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	176 </outputs>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	177
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	178 <trackster_conf>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	179 <action name="global_model" output_name="total_map_mass"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	180 </trackster_conf>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	181 <tests>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	182 <!--
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	183 Simple test that uses test data included with cufflinks.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	184 -->
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	185 <test>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	186 <param name="input" value="cufflinks_in.bam"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	187 <param name="max_intron_len" value="300000"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	188 <param name="min_isoform_fraction" value="0.05"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	189 <param name="pre_mrna_fraction" value="0.05"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	190 <param name="use_ref" value="No"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	191 <param name="do_bias_correction" value="No"/>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	192 <param name="multiread_correct" value="No"/>
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	193 <param name="length_correction" value=""/>
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	194 <param name="use_advanced_settings" value="No" />
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	195 <output name="genes_expression" ftype="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/>
83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	196 <output name="transcripts_expression" ftype="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	197 <output name="assembled_isoforms" file="cufflinks_out1.gtf"/>
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	198 <output name="total_map_mass" file="cufflinks_out4.txt"/>
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	199 <output name="skipped" file="cufflinks_out4.gtf"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	200 </test>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	201 </tests>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	202
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	203 <help>
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	204 Cufflinks Overview
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	205
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	206 Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. 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
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	207
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	208 .. _Cufflinks: http://cole-trapnell-lab.github.io/cufflinks/
5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	209
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	210 ------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	211
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	212 Know what you are doing
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	213
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	214 .. class:: warningmark
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	215
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	216 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.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	217
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	218 .. __: http://cole-trapnell-lab.github.io/cufflinks/cufflinks/
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	219
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	220 ------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	221
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	222 Input formats
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	223
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	224 Cufflinks takes a text file of SAM alignments as input. The RNA-Seq read mapper TopHat produces output in this format, and is recommended for use with Cufflinks. However Cufflinks will accept SAM alignments generated by any read mapper. Here's an example of an alignment Cufflinks will accept::
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	225
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	226 s6.25mer.txt-913508 16 chr1 4482736 255 14M431N11M * 0 0 \
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	227 CAAGATGCTAGGCAAGTCTTGGAAG IIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:-
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	228
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	229 Note the use of the custom tag XS. This attribute, which must have a value of "+" or "-", indicates which strand the RNA that produced this read came from. While this tag can be applied to any alignment, including unspliced ones, it must be present for all spliced alignment records (those with a 'N' operation in the CIGAR string).
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	230 The SAM file supplied to Cufflinks must be sorted by reference position. If you aligned your reads with TopHat, your alignments will be properly sorted already. If you used another tool, you may want to make sure they are properly sorted as follows::
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	231
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	232 sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	233
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	234 NOTE: Cufflinks currently only supports SAM alignments with the CIGAR match ('M') and reference skip ('N') operations. Support for the other operations, such as insertions, deletions, and clipping, will be added in the future.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	235
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	236 ------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	237
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	238 Outputs
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	239
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	240 Cufflinks produces three output files:
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	241
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	242 Transcripts and Genes:
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	243
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	244 This GTF file contains Cufflinks' assembled isoforms. The first 7 columns are standard GTF, and the last column contains attributes, some of which are also standardized (e.g. gene_id, transcript_id). There one GTF record per row, and each record represents either a transcript or an exon within a transcript. The columns are defined as follows::
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	245
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	246 Column number Column name Example Description
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	247 -----------------------------------------------------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	248 1 seqname chrX Chromosome or contig name
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	249 2 source Cufflinks The name of the program that generated this file (always 'Cufflinks')
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	250 3 feature exon The type of record (always either "transcript" or "exon").
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	251 4 start 77696957 The leftmost coordinate of this record (where 0 is the leftmost possible coordinate)
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	252 5 end 77712009 The rightmost coordinate of this record, inclusive.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	253 6 score 77712009 The most abundant isoform for each gene is assigned a score of 1000. Minor isoforms are scored by the ratio (minor FPKM/major FPKM)
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	254 7 strand + Cufflinks' guess for which strand the isoform came from. Always one of '+', '-' '.'
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	255 7 frame . Cufflinks does not predict where the start and stop codons (if any) are located within each transcript, so this field is not used.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	256 8 attributes See below
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	257
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	258 Each GTF record is decorated with the following attributes::
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	259
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	260 Attribute Example Description
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	261 -----------------------------------------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	262 gene_id CUFF.1 Cufflinks gene id
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	263 transcript_id CUFF.1.1 Cufflinks transcript id
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	264 FPKM 101.267 Isoform-level relative abundance in Reads Per Kilobase of exon model per Million mapped reads
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	265 frac 0.7647 Reserved. Please ignore, as this attribute may be deprecated in the future
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	266 conf_lo 0.07 Lower bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, lower bound = FPKM * (1.0 - conf_lo)
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	267 conf_hi 0.1102 Upper bound of the 95% confidence interval of the abundance of this isoform, as a fraction of the isoform abundance. That is, upper bound = FPKM * (1.0 + conf_lo)
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	268 cov 100.765 Estimate for the absolute depth of read coverage across the whole transcript
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	269
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	270 Transcripts only:
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	271 This file is simply a tab delimited file containing one row per transcript and with columns containing the attributes above. There are a few additional attributes not in the table above, but these are reserved for debugging, and may change or disappear in the future.
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	272
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	273 Genes only:
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	274 This file contains gene-level coordinates and expression values.
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	275
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	276 -------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	277
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	278 Cufflinks settings
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	279
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	280 All of the options have a default value. You can change any of them. Most of the options in Cufflinks have been implemented here.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	281
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	282 ------
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	283
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	284 Cufflinks parameter list
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	285
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	286 This is a list of implemented Cufflinks options::
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	287
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	288 -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	289 -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	290 -I INT The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000.
7 5346d5eea8b1 Uploaded devteam parents: 6 diff changeset	291 -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene.
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	292 -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%.
10 83bec71c5c9f planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit eb18f691975ef9539b5ebd4f118343c8ad967a1f devteam parents: 7 diff changeset	293 -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	294 -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts.
b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	295 </help>
12 d080005cffe1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cufflinks commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd" iuc parents: 11 diff changeset	296 <expand macro="citations"/>
0 b50aacc8ae49 Uploaded tool tarball. devteam parents: diff changeset	297 </tool>

Mercurial > repos > devteam > cufflinks

annotate cufflinks_wrapper.xml @ 12:d080005cffe1 draft default tip