stringtie: stringtie.xml annotate

annotate stringtie.xml @ 14:0f5a352b3f04 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65beed7b9259920d3fdb293a1c7060860bd83594

author	iuc
date	Tue, 21 Mar 2017 03:07:08 -0400
parents	f70601406e0e
children	457d00d0005d

rev	line source
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	1 <tool id="stringtie" name="StringTie" version="1.2.3">
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>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	3 <macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	4 <import>macros.xml</import>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	5 </macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	6 <expand macro="requirements" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	7 <expand macro="stdio" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	8 <expand macro="version_command" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	9 <command>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	10 <![CDATA[
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	11 #if $input_bam.metadata.ftype == 'sam':
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	12 samtools sort -@ \${GALAXY_SLOTS:-1} "$input_bam" \| stringtie
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	13 #else
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	14 stringtie "$input_bam"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	15 #end if
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	16 -o "$output_gtf"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	17 -p "\${GALAXY_SLOTS:-1}"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	18 #if str($guide.use_guide) == 'yes':
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	19 -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	20 #if $guide.output_ballgown:
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	21 -b .
11 52f55ad3dee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 46636ba3d63d34e9ee30a2e0ee28cca0213628c8 iuc parents: 10 diff changeset	22 #end if
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	23 #end if
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	24 #if str($option_set.options) == 'advanced':
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	25 -l "$option_set.name_prefix"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	26 -f "$option_set.fraction"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	27 -m "$option_set.min_tlen"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	28 -a "$option_set.min_anchor_len"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	29 -j "$option_set.min_anchor_cov"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	30 -c "$option_set.min_bundle_cov"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	31 -g "$option_set.bdist"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	32 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	33 #if $option_set.abundance_estimation:
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	34 -A "$gene_abundance_estimation"
11 52f55ad3dee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 46636ba3d63d34e9ee30a2e0ee28cca0213628c8 iuc parents: 10 diff changeset	35 #end if
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	36 #if str($option_set.omit_sequences).strip() != "":
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	37 -x "$option_set.omit_sequences"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	38 #end if
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	39 #end if
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	40 ]]>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	41 </command>
5 8836aad67a33 Uploaded iuc parents: diff changeset	42 <inputs>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	43 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	44 <conditional name="guide">
8836aad67a33 Uploaded iuc parents: diff changeset	45 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
8836aad67a33 Uploaded iuc parents: diff changeset	46 <option value="yes">Use GFF</option>
8836aad67a33 Uploaded iuc parents: diff changeset	47 <option selected="True" value="no">Do not use GFF</option>
8836aad67a33 Uploaded iuc parents: diff changeset	48 </param>
8836aad67a33 Uploaded iuc parents: diff changeset	49 <when value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	50 <when value="yes">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	51 <param argument="-G" format="gtf,gff3" help="" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	52 <param argument="-e" falsevalue="" help="" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	53 <param argument="-b" falsevalue="" help="" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	54 </when>
8836aad67a33 Uploaded iuc parents: diff changeset	55 </conditional>
8836aad67a33 Uploaded iuc parents: diff changeset	56 <conditional name="option_set">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	57 <param help="" label="Options" name="options" type="select">
5 8836aad67a33 Uploaded iuc parents: diff changeset	58 <option selected="True" value="default">Use defaults</option>
8836aad67a33 Uploaded iuc parents: diff changeset	59 <option value="advanced">Specify advanced options</option>
8836aad67a33 Uploaded iuc parents: diff changeset	60 </param>
8836aad67a33 Uploaded iuc parents: diff changeset	61 <when value="default" />
8836aad67a33 Uploaded iuc parents: diff changeset	62 <when value="advanced">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	63 <param argument="-t" falsevalue="" help="" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	64 <param argument="-S" falsevalue="" help="" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	65 <param argument="-l" help="" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	66 <param argument="-f" help="" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	67 <param argument="-m" help="" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	68 <param argument="-a" help="" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	69 <param argument="-j" help="" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	70 <param argument="-c" help="" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	71 <param argument="-g" help="" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	72 <param argument="-M" help="" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	73 <param argument="-x" help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" name="omit_sequences" type="text" value="" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	74 <param argument="-A" falsevalue="" help="" label="Additional gene abundance estimation output file" name="abundance_estimation" truevalue="-A" type="boolean" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	75 <param argument="-u" falsevalue="" help="" label="Disable multi-mapping correction" name="multi_mapping" truevalue="-u" type="boolean" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	76 </when>
8836aad67a33 Uploaded iuc parents: diff changeset	77 </conditional>
8836aad67a33 Uploaded iuc parents: diff changeset	78 </inputs>
8836aad67a33 Uploaded iuc parents: diff changeset	79 <outputs>
8836aad67a33 Uploaded iuc parents: diff changeset	80 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	81 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	82 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	83 </data>
5 8836aad67a33 Uploaded iuc parents: diff changeset	84 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	85 <filter>guide['use_guide'] == 'yes'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	86 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	87 <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	88 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	89 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	90 <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	91 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	92 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	93 <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	94 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	95 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	96 <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	97 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	98 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	99 <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	100 <filter>guide['use_guide'] == 'yes' and guide['output_ballgown']</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	101 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	102 </outputs>
8836aad67a33 Uploaded iuc parents: diff changeset	103 <tests>
8836aad67a33 Uploaded iuc parents: diff changeset	104 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	105 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	106 <param name="use_guide" value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	107 <param name="options" value="default" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	108 <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	109 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	110 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	111 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	112 <param name="use_guide" value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	113 <param name="options" value="advanced" />
8836aad67a33 Uploaded iuc parents: diff changeset	114 <param name="fraction" value="0.17" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	115 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	116 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	117 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	118 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	119 <param name="use_guide" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	120 <param name="guide_gff" value="stringtie_in.gtf" />
8836aad67a33 Uploaded iuc parents: diff changeset	121 <param name="options" value="default" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	122 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	123 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	124 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	125 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	126 <param name="use_guide" 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="advanced" />
8836aad67a33 Uploaded iuc parents: diff changeset	129 <param name="fraction" value="0.17" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	130 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	131 </test>
8836aad67a33 Uploaded iuc parents: diff changeset	132 <test>
8836aad67a33 Uploaded iuc parents: diff changeset	133 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
8836aad67a33 Uploaded iuc parents: diff changeset	134 <param name="use_guide" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	135 <param name="output_ballgown" value="yes" />
8836aad67a33 Uploaded iuc parents: diff changeset	136 <param name="guide_gff" value="stringtie_in.gtf" />
8836aad67a33 Uploaded iuc parents: diff changeset	137 <param name="options" value="default" />
8836aad67a33 Uploaded iuc parents: diff changeset	138 <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
8836aad67a33 Uploaded iuc parents: diff changeset	139 <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
8836aad67a33 Uploaded iuc parents: diff changeset	140 <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
8836aad67a33 Uploaded iuc parents: diff changeset	141 <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
8836aad67a33 Uploaded iuc parents: diff changeset	142 <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	143 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	144 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
8836aad67a33 Uploaded iuc parents: diff changeset	145 </test>
10 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 <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	148 <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	149 <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	150 <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	151 <param name="fraction" value="0.17" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	152 <param name="abundance_estimation" value="True" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	153 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	154 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	155 </test>
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	156 <test>
ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	157 <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	158 <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	159 <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	160 <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	161 <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	162 <param name="c" value="test_chromosome" />
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	163 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" 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	164 </test>
5 8836aad67a33 Uploaded iuc parents: diff changeset	165 </tests>
8836aad67a33 Uploaded iuc parents: diff changeset	166 <help>
8836aad67a33 Uploaded iuc parents: diff changeset	167 <![CDATA[
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	168
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	169 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	170
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	171 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	172
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	173 .. _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	174
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	175 ------
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	176
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	177 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	178
5 8836aad67a33 Uploaded iuc parents: diff changeset	179 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
8836aad67a33 Uploaded iuc parents: diff changeset	180 -l name prefix for output transcripts (default: STRG)
8836aad67a33 Uploaded iuc parents: diff changeset	181 -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	182 -m minimum assembled transcript length (default: 200)
5 8836aad67a33 Uploaded iuc parents: diff changeset	183 -o output path/file name for the assembled transcripts GTF (default: stdout)
8836aad67a33 Uploaded iuc parents: diff changeset	184 -a minimum anchor length for junctions (default: 10)
8836aad67a33 Uploaded iuc parents: diff changeset	185 -j minimum junction coverage (default: 1)
8836aad67a33 Uploaded iuc parents: diff changeset	186 -t disable trimming of predicted transcripts based on coverage
8836aad67a33 Uploaded iuc parents: diff changeset	187 (default: coverage trimming is enabled)
8836aad67a33 Uploaded iuc parents: diff changeset	188 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
8836aad67a33 Uploaded iuc parents: diff changeset	189 -v verbose (log bundle processing details)
8836aad67a33 Uploaded iuc parents: diff changeset	190 -g gap between read mappings triggering a new bundle (default: 50)
8836aad67a33 Uploaded iuc parents: diff changeset	191 -C output file with reference transcripts that are covered by reads
8836aad67a33 Uploaded iuc parents: diff changeset	192 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
8836aad67a33 Uploaded iuc parents: diff changeset	193 -p number of threads (CPUs) to use (default: 1)
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	194 -A gene abundance estimation output file
5 8836aad67a33 Uploaded iuc parents: diff changeset	195 -B enable output of Ballgown table files which will be created in the
8836aad67a33 Uploaded iuc parents: diff changeset	196 same directory as the output GTF (requires -G, -o recommended)
8836aad67a33 Uploaded iuc parents: diff changeset	197 -b enable output of Ballgown table files but these files will be
8836aad67a33 Uploaded iuc parents: diff changeset	198 created under the directory path given as <dir_path>
8836aad67a33 Uploaded iuc parents: diff changeset	199 -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	200 -x do not assemble any transcripts on these reference sequence(s)
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	201 -u no multi-mapping correction default: false)
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	202
5 8836aad67a33 Uploaded iuc parents: diff changeset	203 ]]>
8836aad67a33 Uploaded iuc parents: diff changeset	204 </help>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	205 <expand macro="citations" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	206 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 14:0f5a352b3f04 draft