stringtie: stringtie.xml annotate

annotate stringtie.xml @ 11:6e45b443ef1f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf

author	iuc
date	Thu, 01 Jun 2017 12:16:04 -0400
parents	c84d44519b2e
children	76d290331481

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" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	9 <command><![CDATA[
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	10 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	11 #if str($guide.use_guide) == 'yes':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	12 ln -s '$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	13 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	14
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	15 #if $input_bam.metadata.ftype == 'sam':
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	16 samtools sort -@ \${GALAXY_SLOTS:-1} '$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	17 #else
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	18 stringtie '$input_bam'
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	19 #end if
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	20
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	21 -o "$output_gtf"
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	22 -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	23 #if str($guide.use_guide) == 'yes':
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	24 -C '$coverage'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	25 -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	26 $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	27 #if $guide.special_outputs != 'no':
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	28 -b ./special_de_output/sample1/
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	29 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	30 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	31 #if str($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	32 -l '$option_set.name_prefix'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	33 -f '$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	34 -m '$option_set.min_tlen'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	35 -a '$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	36 -j '$option_set.min_anchor_cov'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	37 -c '$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	38 -g '$option_set.bdist'
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	39 -M '$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	40 #if $option_set.abundance_estimation:
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	41 -A "$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	42 #end if
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	43 #if str($option_set.omit_sequences).strip() != "":
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	44 -x '$option_set.omit_sequences'
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	45 #end if
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
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	47
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	48 #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	49 #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	50 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	51 prepDE.py
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	52 -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	53 -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	54 -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	55 -l $guide.special_outputs.read_length
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	56 #if str($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	57 -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	58 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	59 #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	60 -c
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	61 --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	62
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 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	65
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	66 #end if
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	67 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	68 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	69 &&
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	70 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	71 #end if
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
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	73 ]]></command>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	74 <inputs>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	75 <param name="input_bam" type="data" format="sam,bam" label="Mapped reads to assemble transcripts from" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	76 <conditional name="guide">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	77 <param name="use_guide" type="select" label="Use GFF file to guide assembly">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	78 <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	79 <option selected="True" value="no">Do not use GFF/GTF</option>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	80 </param>
62d212192002 Imported from capsule None iuc parents: diff changeset	81 <when value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	82 <when value="yes">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	83 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	84 label="Reference annotation to use for guiding the assembly process" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	85 <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue=""
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	86 label="Perform abundance estimation only of input transcripts" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	87 <conditional name="special_outputs">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	88 <param name="special_outputs_select" type="select" label="Output additional files for use in...">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	89 <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	90 <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	91 <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	92 </param>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	93 <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	94 <when value="deseq2">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	95 <param name="read_length" type="integer" value="75" label="Average read length" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	96 <param name="clustering" type="boolean" truevalue="--cluster" falsevalue="" label="Whether to cluster genes that overlap with different gene IDs" help="ignoring ones with geneID pattern" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	97 </when>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	98 <when value="no" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	99 </conditional>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	100 </when>
62d212192002 Imported from capsule None iuc parents: diff changeset	101 </conditional>
62d212192002 Imported from capsule None iuc parents: diff changeset	102 <conditional name="option_set">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	103 <param name="options" type="select" label="Options">
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	104 <option selected="True" value="default">Use defaults</option>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	105 <option value="advanced">Specify advanced options</option>
62d212192002 Imported from capsule None iuc parents: diff changeset	106 </param>
62d212192002 Imported from capsule None iuc parents: diff changeset	107 <when value="default" />
62d212192002 Imported from capsule None iuc parents: diff changeset	108 <when value="advanced">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	109 <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue=""
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	110 label="Disable trimming of predicted transcripts based on coverage" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	111 <param name="sensitive" argument="-S" type="boolean" truevalue="-S" falsevalue=""
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	112 label="Increase sensitivity" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	113 <param name="name_prefix" argument="-l" type="text" value="STRG" label="Name prefix for output transcripts" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	114 <param name="fraction" argument="-f" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	115 <param name="min_tlen" argument="-m" type="integer" value="200" label="Minimum assembled transcript length" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	116 <param name="min_anchor_len" argument="-a" type="integer" value="10" label="Minimum anchor length for junctions" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	117 <param name="min_anchor_cov" argument="-j" type="integer" value="1" label="Minimum junction coverage" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	118 <param name="min_bundle_cov" argument="-c" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	119 <param name="bdist" argument="-g" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	120 <param name="bundle_fraction" argument="-M" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	121 <param name="omit_sequences" argument="-x" type="text" value=""
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	122 label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	123 <param name="abundance_estimation" argument="-A" type="boolean" truevalue="-A" falsevalue=""
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	124 label="Additional gene abundance estimation output file" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	125 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue=""
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	126 label="Disable multi-mapping correction" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	127 </when>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	128 </conditional>
62d212192002 Imported from capsule None iuc parents: diff changeset	129 </inputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	130 <outputs>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	131 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	132 <data name="gene_abundance_estimation" format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates">
7 e3f369973054 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 6 diff changeset	133 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	134 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	135 <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
7 e3f369973054 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 6 diff changeset	136 <filter>guide['use_guide'] == 'yes'</filter>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	137 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	138 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	139 label="${tool.name} on ${on_string}: exon-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	140 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	141 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	142 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	143 label="${tool.name} on ${on_string}: intron-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	144 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	145 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	146 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	147 label="${tool.name} on ${on_string}: transcript-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	148 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	149 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	150 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	151 label="${tool.name} on ${on_string}: exon to transcript mapping">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	152 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	153 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	154 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	155 label="${tool.name} on ${on_string}: intron to transcript mapping">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	156 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	157 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	158 <data name="gene_counts" format="tabular" from_work_dir="gene_cout_matrix.tsv"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	159 label="${tool.name} on ${on_string}: Gene counts">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	160 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	161 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	162 <data name="transcript_counts" format="tabular" from_work_dir="transcripts_count_matrix.tsv"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	163 label="${tool.name} on ${on_string}: Transcript counts">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	164 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	165 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	166 <data name="legend" format="tabular" from_work_dir="legend.tsv"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	167 label="${tool.name} on ${on_string}: legend">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	168 <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	169 </data>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	170 </outputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	171 <tests>
62d212192002 Imported from capsule None iuc parents: diff changeset	172 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	173 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	174 <param name="use_guide" value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	175 <param name="options" value="default" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	176 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	177 </test>
62d212192002 Imported from capsule None iuc parents: diff changeset	178 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	179 <param name="input_bam" ftype="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="advanced" />
62d212192002 Imported from capsule None iuc parents: diff changeset	182 <param name="fraction" value="0.17" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	183 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	184 </test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	185 <test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	186 <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	187 <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	188 <param name="special_outputs_select" value="no" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	189 <param name="guide_gff" value="stringtie_in.gtf" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	190 <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	191 <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	192 </test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	193 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	194 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	195 <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	196 <param name="special_outputs_select" value="no" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	197 <param name="guide_gff" value="stringtie_in.gtf" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	198 <param name="options" value="advanced" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	199 <param name="fraction" value="0.17" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	200 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	201 </test>
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	202 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	203 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	204 <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	205 <param name="special_outputs_select" value="ballgown" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	206 <param name="guide_gff" value="stringtie_in.gtf" />
9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	207 <param name="options" value="default" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	208 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	209 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	210 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	211 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	212 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	213 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	214 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gff3" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	215 </test>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	216 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	217 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	218 <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	219 <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	220 <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	221 <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	222 <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	223 <param name="clustering" value="True" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	224 <output name="gene_counts" file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	225 <output name="transcript_counts" file="./deseq2/transcript_counts.tsv" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	226 <output name="legend" file="./deseq2/legend.tsv" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	227 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	228 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gff3" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	229 </test>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	230 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	231 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	232 <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	233 <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	234 <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	235 <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	236 <param name="abundance_estimation" value="True" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	237 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	238 <output name="gene_abundance_estimation" file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	239 </test>
f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	240 <test>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	241 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	242 <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	243 <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	244 <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	245 <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	246 <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	247 <param name="c" value="test_chromosome" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	248 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	249 </test>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	250 </tests>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	251 <help><![CDATA[
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	252 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	253
520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	254 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	255
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	256 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	257 ]]></help>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	258 <expand macro="citations" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	259 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 11:6e45b443ef1f draft