stringtie: stringtie.xml annotate

annotate stringtie.xml @ 10:ce5e12ebb972 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a

author	iuc
date	Wed, 21 Oct 2015 16:06:19 -0400
parents	bb9b52023df4
children	52f55ad3dee2

rev	line source
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	1 <tool id="stringtie" name="StringTie" version="1.1.0">
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	2 <description>transcript assembly and quantification</description>
5 8836aad67a33 Uploaded iuc parents: diff changeset	3 <requirements>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	4 <requirement type="package" version="1.1.0">stringtie</requirement>
5 8836aad67a33 Uploaded iuc parents: diff changeset	5 </requirements>
8836aad67a33 Uploaded iuc parents: diff changeset	6 <command><![CDATA[
8836aad67a33 Uploaded iuc parents: diff changeset	7 stringtie "$input_bam"
8836aad67a33 Uploaded iuc parents: diff changeset	8 -o "$output_gtf"
8836aad67a33 Uploaded iuc parents: diff changeset	9 -p "\${GALAXY_SLOTS:-1}"
8836aad67a33 Uploaded iuc parents: diff changeset	10 #if str($guide.use_guide) == 'yes':
8836aad67a33 Uploaded iuc parents: diff changeset	11 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
8836aad67a33 Uploaded iuc parents: diff changeset	12 #if str($guide.output_ballgown) == '-b':
8836aad67a33 Uploaded iuc parents: diff changeset	13 $guide.output_ballgown `pwd`
8836aad67a33 Uploaded iuc parents: diff changeset	14 #end if
8836aad67a33 Uploaded iuc parents: diff changeset	15 #end if
8836aad67a33 Uploaded iuc parents: diff changeset	16 #if str($option_set.options) == 'advanced':
8836aad67a33 Uploaded iuc parents: diff changeset	17 -l "$option_set.name_prefix"
8836aad67a33 Uploaded iuc parents: diff changeset	18 -f "$option_set.fraction"
8836aad67a33 Uploaded iuc parents: diff changeset	19 -m "$option_set.min_tlen"
8836aad67a33 Uploaded iuc parents: diff changeset	20 -a "$option_set.min_anchor_len"
8836aad67a33 Uploaded iuc parents: diff changeset	21 -j "$option_set.min_anchor_cov"
8836aad67a33 Uploaded iuc parents: diff changeset	22 -c "$option_set.min_bundle_cov"
9 bb9b52023df4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf iuc parents: 8 diff changeset	23 -g "$option_set.bdist"
5 8836aad67a33 Uploaded iuc parents: diff changeset	24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	25 #if $option_set.A:
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	26 -A "$gene_abundance_estimation"
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	27 #end if
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	28 #if str($option_set.x).strip() != "":
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	29 -x "$option_set.x"
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	30 #end if
5 8836aad67a33 Uploaded iuc parents: diff changeset	31 #end if
8836aad67a33 Uploaded iuc parents: diff changeset	32 ]]>
8836aad67a33 Uploaded iuc parents: diff changeset	33 </command>
8836aad67a33 Uploaded iuc parents: diff changeset	34 <inputs>
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	35 <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	36 <conditional name="guide">
8836aad67a33 Uploaded iuc parents: diff changeset	37 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
8836aad67a33 Uploaded iuc parents: diff changeset	38 <option value="yes">Use GFF</option>
8836aad67a33 Uploaded iuc parents: diff changeset	39 <option selected="True" value="no">Do not use GFF</option>
8836aad67a33 Uploaded iuc parents: diff changeset	40 </param>
8836aad67a33 Uploaded iuc parents: diff changeset	41 <when value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	42 <when value="yes">
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	43 <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	44 <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	45 <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	46 </when>
8836aad67a33 Uploaded iuc parents: diff changeset	47 </conditional>
8836aad67a33 Uploaded iuc parents: diff changeset	48 <conditional name="option_set">
8836aad67a33 Uploaded iuc parents: diff changeset	49 <param label="Options" name="options" type="select">
8836aad67a33 Uploaded iuc parents: diff changeset	50 <option selected="True" value="default">Use defaults</option>
8836aad67a33 Uploaded iuc parents: diff changeset	51 <option value="advanced">Specify advanced options</option>
8836aad67a33 Uploaded iuc parents: diff changeset	52 </param>
8836aad67a33 Uploaded iuc parents: diff changeset	53 <when value="default" />
8836aad67a33 Uploaded iuc parents: diff changeset	54 <when value="advanced">
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	55 <param falsevalue="" help="-t" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	56 <param falsevalue="" help="-S" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	57 <param help="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	58 <param help="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	59 <param help="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	60 <param help="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	61 <param help="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	62 <param help="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	63 <param help="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	64 <param help="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	65 <param argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	66 <param argument="-A" truevalue="-A" falsevalue="" type="boolean" help="" label="Additional gene abundance estimation output file" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	67 </when>
8836aad67a33 Uploaded iuc parents: diff changeset	68 </conditional>
8836aad67a33 Uploaded iuc parents: diff changeset	69 </inputs>
8836aad67a33 Uploaded iuc parents: diff changeset	70 <outputs>
8836aad67a33 Uploaded iuc parents: diff changeset	71 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	72 <data format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	73 <filter>option_set['A']</filter>
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	74 </data>
5 8836aad67a33 Uploaded iuc parents: diff changeset	75 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
8836aad67a33 Uploaded iuc parents: diff changeset	76 <filter>guide['use_guide'] == "yes"</filter>
8836aad67a33 Uploaded iuc parents: diff changeset	77 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	78 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
8836aad67a33 Uploaded iuc parents: diff changeset	79 <filter>guide['output_ballgown']</filter>
8836aad67a33 Uploaded iuc parents: diff changeset	80 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	81 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
8836aad67a33 Uploaded iuc parents: diff changeset	82 <filter>guide['output_ballgown']</filter>
8836aad67a33 Uploaded iuc parents: diff changeset	83 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	84 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
8836aad67a33 Uploaded iuc parents: diff changeset	85 <filter>guide['output_ballgown']</filter>
8836aad67a33 Uploaded iuc parents: diff changeset	86 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	87 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
8836aad67a33 Uploaded iuc parents: diff changeset	88 <filter>guide['output_ballgown']</filter>
8836aad67a33 Uploaded iuc parents: diff changeset	89 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	90 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
8836aad67a33 Uploaded iuc parents: diff changeset	91 <filter>guide['output_ballgown']</filter>
8836aad67a33 Uploaded iuc parents: diff changeset	92 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	93 </outputs>
8836aad67a33 Uploaded iuc parents: diff changeset	94 <tests>
8836aad67a33 Uploaded iuc parents: diff changeset	95 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	96 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	97 <param name="use_guide" value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	98 <param name="options" value="default" />
9 bb9b52023df4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf iuc parents: 8 diff changeset	99 <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	100 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	101 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	102 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	103 <param name="use_guide" value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	104 <param name="options" value="advanced" />
8836aad67a33 Uploaded iuc parents: diff changeset	105 <param name="fraction" value="0.17" />
9 bb9b52023df4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf iuc parents: 8 diff changeset	106 <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	107 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	108 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	109 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	110 <param name="use_guide" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	111 <param name="guide_gff" value="stringtie_in.gtf" />
8836aad67a33 Uploaded iuc parents: diff changeset	112 <param name="options" value="default" />
9 bb9b52023df4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf iuc parents: 8 diff changeset	113 <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	114 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	115 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	116 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	117 <param name="use_guide" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	118 <param name="guide_gff" value="stringtie_in.gtf" />
8836aad67a33 Uploaded iuc parents: diff changeset	119 <param name="options" value="advanced" />
8836aad67a33 Uploaded iuc parents: diff changeset	120 <param name="fraction" value="0.17" />
9 bb9b52023df4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf iuc parents: 8 diff changeset	121 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	122 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	123 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	124 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	125 <param name="use_guide" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	126 <param name="output_ballgown" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	127 <param name="guide_gff" value="stringtie_in.gtf" />
8836aad67a33 Uploaded iuc parents: diff changeset	128 <param name="options" value="default" />
8836aad67a33 Uploaded iuc parents: diff changeset	129 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
8836aad67a33 Uploaded iuc parents: diff changeset	130 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
8836aad67a33 Uploaded iuc parents: diff changeset	131 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
8836aad67a33 Uploaded iuc parents: diff changeset	132 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
8836aad67a33 Uploaded iuc parents: diff changeset	133 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
9 bb9b52023df4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit ba7b53894c61fea9a93550f865e9ed2753a904cf iuc parents: 8 diff changeset	134 <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	135 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
8836aad67a33 Uploaded iuc parents: diff changeset	136 </test>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	137 <test>
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	138 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	139 <param name="use_guide" value="yes" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	140 <param name="guide_gff" value="stringtie_in.gtf" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	141 <param name="options" value="advanced" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	142 <param name="fraction" value="0.17" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	143 <param name="A" value="True" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	144 <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	145 <output file="stringtie_out6.gtf" ftype="tabular" name="gene_abundance_estimation" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	146 </test>
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	147 <test>
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	148 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	149 <param name="use_guide" value="yes" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	150 <param name="guide_gff" value="stringtie_in.gtf" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	151 <param name="options" value="advanced" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	152 <param name="fraction" value="0.15" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	153 <param name="c" value="test_chromosome" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	154 <output file="stringtie_out7.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	155 </test>
5 8836aad67a33 Uploaded iuc parents: diff changeset	156 </tests>
8836aad67a33 Uploaded iuc parents: diff changeset	157 <help>
8836aad67a33 Uploaded iuc parents: diff changeset	158 <![CDATA[
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	159
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	160 What it does?
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	161
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	162 StringTie_ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.
5 8836aad67a33 Uploaded iuc parents: diff changeset	163
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	164 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	165
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	166 ------
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	167
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	168 StringTie has the following options::
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	169
5 8836aad67a33 Uploaded iuc parents: diff changeset	170 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
8836aad67a33 Uploaded iuc parents: diff changeset	171 -l name prefix for output transcripts (default: STRG)
8836aad67a33 Uploaded iuc parents: diff changeset	172 -f minimum isoform fraction (default: 0.1)
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	173 -m minimum assembled transcript length (default: 200)
5 8836aad67a33 Uploaded iuc parents: diff changeset	174 -o output path/file name for the assembled transcripts GTF (default: stdout)
8836aad67a33 Uploaded iuc parents: diff changeset	175 -a minimum anchor length for junctions (default: 10)
8836aad67a33 Uploaded iuc parents: diff changeset	176 -j minimum junction coverage (default: 1)
8836aad67a33 Uploaded iuc parents: diff changeset	177 -t disable trimming of predicted transcripts based on coverage
8836aad67a33 Uploaded iuc parents: diff changeset	178 (default: coverage trimming is enabled)
8836aad67a33 Uploaded iuc parents: diff changeset	179 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
8836aad67a33 Uploaded iuc parents: diff changeset	180 -v verbose (log bundle processing details)
8836aad67a33 Uploaded iuc parents: diff changeset	181 -g gap between read mappings triggering a new bundle (default: 50)
8836aad67a33 Uploaded iuc parents: diff changeset	182 -C output file with reference transcripts that are covered by reads
8836aad67a33 Uploaded iuc parents: diff changeset	183 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
8836aad67a33 Uploaded iuc parents: diff changeset	184 -p number of threads (CPUs) to use (default: 1)
8836aad67a33 Uploaded iuc parents: diff changeset	185 -B enable output of Ballgown table files which will be created in the
8836aad67a33 Uploaded iuc parents: diff changeset	186 same directory as the output GTF (requires -G, -o recommended)
8836aad67a33 Uploaded iuc parents: diff changeset	187 -b enable output of Ballgown table files but these files will be
8836aad67a33 Uploaded iuc parents: diff changeset	188 created under the directory path given as <dir_path>
8836aad67a33 Uploaded iuc parents: diff changeset	189 -e only estimates the abundance of given reference transcripts (requires -G)
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	190 -A gene abundance estimation output file
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	191 -x do not assemble any transcripts on these reference sequence(s)
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	192
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	193
5 8836aad67a33 Uploaded iuc parents: diff changeset	194 ]]>
8836aad67a33 Uploaded iuc parents: diff changeset	195 </help>
8836aad67a33 Uploaded iuc parents: diff changeset	196 <citations>
8836aad67a33 Uploaded iuc parents: diff changeset	197 <citation type="doi">doi:10.1038/nbt.3122</citation>
8836aad67a33 Uploaded iuc parents: diff changeset	198 </citations>
8836aad67a33 Uploaded iuc parents: diff changeset	199 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 10:ce5e12ebb972 draft