stringtie: stringtie.xml annotate

annotate stringtie.xml @ 10:c84d44519b2e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103

author	iuc
date	Tue, 04 Apr 2017 12:58:27 -0400
parents	e3f369973054
children	6e45b443ef1f

rev	line source
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	1 <tool id="stringtie" name="StringTie" version="1.3.3">
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	2 <description>transcript assembly and quantification</description>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	3 <macros>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	4 <import>macros.xml</import>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	5 </macros>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	6 <expand macro="requirements" />
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	7 <expand macro="stdio" />
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	8 <expand macro="version_command" />
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	9 <command>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	10 <![CDATA[
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	11 mkdir -p ./special_de_output/sample1/ &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	12 #if str($guide.use_guide) == 'yes':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	13 ln -s '$guide.guide_gff' ./special_de_output/sample1/guide.gtf &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	14 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	15
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	16 #if $input_bam.metadata.ftype == 'sam':
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	17 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' \| stringtie
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	18 #else
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	19 stringtie '$input_bam'
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	20 #end if
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	21
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	22 -o "$output_gtf"
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	23 -p "\${GALAXY_SLOTS:-1}"
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	24 #if str($guide.use_guide) == 'yes':
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	25 -C '$coverage'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	26 -G '$guide.guide_gff'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	27 $guide.input_estimation
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	28 #if $guide.special_outputs != 'no':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	29 -b ./special_de_output/sample1/
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	30 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	31 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	32 #if str($option_set.options) == 'advanced':
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	33 -l '$option_set.name_prefix'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	34 -f '$option_set.fraction'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	35 -m '$option_set.min_tlen'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	36 -a '$option_set.min_anchor_len'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	37 -j '$option_set.min_anchor_cov'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	38 -c '$option_set.min_bundle_cov'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	39 -g '$option_set.bdist'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	40 -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	41 #if $option_set.abundance_estimation:
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	42 -A "$gene_abundance_estimation"
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	43 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	44 #if str($option_set.omit_sequences).strip() != "":
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	45 -x "$option_set.omit_sequences"
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	46 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	47 #end if
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	48
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	49 #if str($guide.use_guide) == 'yes':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	50 #if $guide.special_outputs.special_outputs_select == 'deseq2':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	51 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	52 prepDE.py
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	53 -i ./special_de_output/
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	54 -g gene_cout_matrix.tsv
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	55 -t transcripts_count_matrix.tsv
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	56 -l $guide.special_outputs.read_length
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	57 #if str($option_set.options) == 'advanced':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	58 -s '$option_set.name_prefix'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	59 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	60 #if $guide.special_outputs.clustering:
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	61 -c
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	62 --legend ./legend.tsv
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	63
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	64 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	65 sed -i.bak 's/,/\t/g' ./legend.tsv
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	66
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	67 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	68 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	69 sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	70 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	71 sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	72 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	73 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	74
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	75 ]]>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	76 </command>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	77 <inputs>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	78 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	79 <conditional name="guide">
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	80 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	81 <option value="yes">Use GFF/GTF</option>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	82 <option selected="True" value="no">Do not use GFF/GTF</option>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	83 </param>
62d212192002 Imported from capsule None iuc parents: diff changeset	84 <when value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	85 <when value="yes">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	86 <param argument="-G" format="gtf,gff3" name="guide_gff" type="data"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	87 help="" label="Reference annotation to use for guiding the assembly process" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	88 <param argument="-e" name="input_estimation" truevalue="-e" type="boolean" falsevalue=""
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	89 help="" label="Perform abundance estimation only of input transcripts" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	90 <conditional name="special_outputs">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	91 <param label="Output additional files for use in..." name="special_outputs_select" type="select">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	92 <option value="ballgown">Ballgown</option>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	93 <option selected="True" value="deseq2">DESeq2/EdgeR</option>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	94 <option value="no">No addional output</option>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	95 </param>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	96 <when value="ballgown" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	97 <when value="deseq2">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	98 <param label="Average read length" name="read_length" type="integer" value="75" help="" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	99 <param label="Whether to cluster genes that overlap with different gene IDs"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	100 name="clustering"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	101 truevalue="--cluster"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	102 type="boolean" help="ignoring ones with geneID pattern" falsevalue="" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	103 </when>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	104 </conditional>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	105 </when>
62d212192002 Imported from capsule None iuc parents: diff changeset	106 </conditional>
62d212192002 Imported from capsule None iuc parents: diff changeset	107 <conditional name="option_set">
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	108 <param help="" label="Options" name="options" type="select">
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	109 <option selected="True" value="default">Use defaults</option>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	110 <option value="advanced">Specify advanced options</option>
62d212192002 Imported from capsule None iuc parents: diff changeset	111 </param>
62d212192002 Imported from capsule None iuc parents: diff changeset	112 <when value="default" />
62d212192002 Imported from capsule None iuc parents: diff changeset	113 <when value="advanced">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	114 <param argument="-t" falsevalue="" name="disable_trimming" truevalue="-t" type="boolean"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	115 label="Disable trimming of predicted transcripts based on coverage" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	116 <param argument="-S" falsevalue=""
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	117 label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	118 <param argument="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	119 <param argument="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	120 <param argument="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	121 <param argument="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	122 <param argument="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	123 <param argument="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	124 <param argument="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	125 <param argument="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	126 <param argument="-x" name="omit_sequences" type="text" value=""
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	127 help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	128 <param argument="-A" falsevalue="" name="abundance_estimation" truevalue="-A" type="boolean"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	129 label="Additional gene abundance estimation output file" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	130 <param argument="-u" falsevalue="" truevalue="-u" type="boolean"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	131 label="Disable multi-mapping correction" name="multi_mapping" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	132 </when>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	133 </conditional>
62d212192002 Imported from capsule None iuc parents: diff changeset	134 </inputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	135 <outputs>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	136 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	137 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
7 e3f369973054 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 6 diff changeset	138 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	139 </data>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	140 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
7 e3f369973054 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 6 diff changeset	141 <filter>guide['use_guide'] == 'yes'</filter>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	142 </data>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	143 <data format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	144 label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	145 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	146 </data>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	147 <data format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	148 label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	149 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	150 </data>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	151 <data format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	152 label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	153 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	154 </data>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	155 <data format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	156 label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	157 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	158 </data>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	159 <data format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	160 label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	161 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	162 </data>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	163
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	164 <data format="tabular" from_work_dir="gene_cout_matrix.tsv"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	165 label="${tool.name} on ${on_string}: Gene counts" name="gene_counts">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	166 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	167 </data>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	168 <data format="tabular" from_work_dir="transcripts_count_matrix.tsv"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	169 label="${tool.name} on ${on_string}: Transcript counts" name="transcript_counts">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	170 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	171 </data>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	172 <data format="tabular" from_work_dir="legend.tsv"
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	173 label="${tool.name} on ${on_string}: legend" name="legend">
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	174 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	175 </data>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	176 </outputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	177 <tests>
62d212192002 Imported from capsule None iuc parents: diff changeset	178 <test>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	179 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	180 <param name="use_guide" value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	181 <param name="options" value="default" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	182 <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	183 </test>
62d212192002 Imported from capsule None iuc parents: diff changeset	184 <test>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	185 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	186 <param name="use_guide" value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	187 <param name="options" value="advanced" />
62d212192002 Imported from capsule None iuc parents: diff changeset	188 <param name="fraction" value="0.17" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	189 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	190 </test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	191 <test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	192 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	193 <param name="use_guide" value="yes" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	194 <param name="special_outputs_select" value="no" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	195 <param name="guide_gff" value="stringtie_in.gtf" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	196 <param name="options" value="default" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	197 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	198 </test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	199 <test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	200 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	201 <param name="use_guide" value="yes" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	202 <param name="special_outputs_select" value="no" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	203 <param name="guide_gff" value="stringtie_in.gtf" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	204 <param name="options" value="advanced" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	205 <param name="fraction" value="0.17" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	206 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	207 </test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	208 <test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	209 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	210 <param name="use_guide" value="yes" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	211 <param name="special_outputs_select" value="ballgown" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	212 <param name="guide_gff" value="stringtie_in.gtf" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	213 <param name="options" value="default" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	214 <output file="./ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	215 <output file="./ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	216 <output file="./ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	217 <output file="./ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	218 <output file="./ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	219 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	220 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	221 </test>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	222 <test>
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	223 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	224 <param name="use_guide" value="yes" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	225 <param name="special_outputs_select" value="deseq2" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	226 <param name="input_estimation" value="True" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	227 <param name="guide_gff" value="stringtie_in.gtf" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	228 <param name="options" value="default" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	229 <param name="clustering" value="True" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	230 <output file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" name="gene_counts" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	231 <output file="./deseq2/transcript_counts.tsv" ftype="tabular" name="transcript_counts" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	232 <output file="./deseq2/legend.tsv" ftype="tabular" name="legend" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	233 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	234 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	235 </test>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	236 <test>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	237 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	238 <param name="use_guide" value="yes" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	239 <param name="guide_gff" value="stringtie_in.gtf" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	240 <param name="options" value="advanced" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	241 <param name="fraction" value="0.17" />
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	242 <param name="abundance_estimation" value="True" />
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	243 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	244 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	245 </test>
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	246 <test>
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	247 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	248 <param name="use_guide" value="yes" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	249 <param name="special_outputs_select" value="no" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	250 <param name="guide_gff" value="stringtie_in.gtf" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	251 <param name="options" value="advanced" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	252 <param name="fraction" value="0.15" />
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	253 <param name="c" value="test_chromosome" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	254 <output file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	255 </test>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	256 </tests>
62d212192002 Imported from capsule None iuc parents: diff changeset	257 <help>
62d212192002 Imported from capsule None iuc parents: diff changeset	258 <![CDATA[
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	259
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	260 What it does?
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	261
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	262 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.
0 62d212192002 Imported from capsule None iuc parents: diff changeset	263
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	264 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	265
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	266 ------
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	267
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	268 StringTie has the following options::
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	269
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	270 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	271 -l name prefix for output transcripts (default: STRG)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	272 -f minimum isoform fraction (default: 0.1)
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	273 -m minimum assembled transcript length (default: 200)
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	274 -o output path/file name for the assembled transcripts GTF (default: stdout)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	275 -a minimum anchor length for junctions (default: 10)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	276 -j minimum junction coverage (default: 1)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	277 -t disable trimming of predicted transcripts based on coverage
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	278 (default: coverage trimming is enabled)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	279 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	280 -v verbose (log bundle processing details)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	281 -g gap between read mappings triggering a new bundle (default: 50)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	282 -C output file with reference transcripts that are covered by reads
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	283 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	284 -p number of threads (CPUs) to use (default: 1)
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	285 -A gene abundance estimation output file
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	286 -B enable output of Ballgown table files which will be created in the
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	287 same directory as the output GTF (requires -G, -o recommended)
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	288 -b enable output of Ballgown table files but these files will be
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	289 created under the directory path given as <dir_path>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	290 -e only estimates the abundance of given reference transcripts (requires -G)
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	291 -x do not assemble any transcripts on these reference sequence(s)
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	292 -u no multi-mapping correction default: false)
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	293
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	294 ]]>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	295 </help>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	296 <expand macro="citations" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	297 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 10:c84d44519b2e draft