stringtie: stringtie.xml annotate

annotate stringtie.xml @ 13:a305d75e13f2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23

author	iuc
date	Thu, 12 Apr 2018 17:30:07 -0400
parents	76d290331481
children	eafd5dc95228

rev	line source
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	1 <tool id="stringtie" name="StringTie" version="1.3.3.2">
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[
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	10 #import re
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	11 mkdir -p ./special_de_output/sample1/ &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	12
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	13 ## Get Guide GTF/GFF if selected
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	14
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	15 #if str($guide.use_guide) == 'yes':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	16 #if $guide.guide_source.guide_gff_select == "history":
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	17 ln -s '$guide.guide_source.ref_hist' guide.gff &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	18 #elif $guide.guide_source.guide_gff_select == "cached":
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	19 ln -s '$guide.guide_source.ref_builtin.fields.path' guide.gff &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	20 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	21 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	22
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	23 #if $input_bam.metadata.ftype == 'sam':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	24 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' \| stringtie
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	25 #else
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	26 stringtie '$input_bam'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	27 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	28
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	29 -o '$output_gtf'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	30 -p "\${GALAXY_SLOTS:-1}"
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	31
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	32 $rna_strandness
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	33
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	34 #if str($guide.use_guide) == 'yes':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	35 -G guide.gff
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	36 #if $guide.coverage_file:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	37 -C '$coverage'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	38 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	39 $guide.input_estimation
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	40 #if $guide.special_outputs != 'no':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	41 -b ./special_de_output/sample1/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	42 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	43 #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	44
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	45 #if $adv.name_prefix:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	46 -l '$adv.name_prefix'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	47 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	48 -f '$adv.fraction'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	49 -m '$adv.min_tlen'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	50 -a '$adv.min_anchor_len'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	51 -j '$adv.min_anchor_cov'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	52 -c '$adv.min_bundle_cov'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	53 -g '$adv.bdist'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	54 -M '$adv.bundle_fraction'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	55 $adv.disable_trimming
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	56 $adv.multi_mapping
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	57 #if $adv.abundance_estimation:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	58 -A '$gene_abundance_estimation'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	59 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	60 #if str($adv.omit_sequences).strip() != "":
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	61 -x '$adv.omit_sequences'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	62 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	63
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	64 #if str($guide.use_guide) == 'yes':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	65 #if $guide.special_outputs.special_outputs_select == 'deseq2':
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	66 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	67 &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	68 ln -s '$output_gtf' ./special_de_output/sample1/output.gtf
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	69 &&
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	70 TAB=\$(printf '\t')
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	71 &&
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	72 CR=\$(printf '\r')
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	73 &&
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	74 prepDE.py
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	75 -i ./special_de_output/
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	76 -g gene_counts.csv
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	77 -t transcript_counts.csv
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	78 -l $guide.special_outputs.read_length
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	79 #if $guide.special_outputs.string:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	80 -s '$guide.special_outputs.string'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	81 #end if
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	82 #if $guide.special_outputs.clustering:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	83 -c
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	84 #if $guide.special_outputs.key:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	85 -k '$guide.special_outputs.key'
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	86 #end if
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	87 --legend '$legend'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	88 > /dev/null
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	89 &&
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	90 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" '$legend'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	91 #else
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	92 > /dev/null
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	93 #end if
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	94
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	95 ## Replace commas with tabs
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	96 &&
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	97 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" gene_counts.csv transcript_counts.csv
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	98 #if $guide.special_outputs.keep_header:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	99 &&
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	100 head -n 1 gene_counts.csv \| sed -e 's/sample1/$escaped_element_identifier/' > '$gene_counts'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	101 &&
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	102 head -n 1 transcript_counts.csv \| sed -e 's/sample1/$escaped_element_identifier/' > '$transcript_counts'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	103 #end if
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	104 ## Sort count files on the first column
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	105 &&
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	106 tail -n +2 gene_counts.csv \| sort -t"\${TAB}" -k1 >> '$gene_counts'
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	107 &&
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	108 tail -n +2 transcript_counts.csv \| sort -t"\${TAB}" -k1 >> '$transcript_counts'
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	109 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	110 #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	111 ]]></command>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	112 <inputs>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	113 <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	114 <param name="rna_strandness" type="select" label="Specify strand information"
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	115 help="Select 'Forward (FR)' if your reads are from a forward-stranded library, 'Reverse (RF)' if your reads are from a reverse-stranded library, or 'Unstranded' if your reads are not from a stranded library. See Help section below for more information. Default: Unstranded">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	116 <option value="" selected="True">Unstranded</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	117 <option value="--fr">Forward (FR)</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	118 <option value="--rf">Reverse (RF)</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	119 </param>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	120 <conditional name="guide">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	121 <param name="use_guide" argument="-G" type="select" label="Use a reference file to guide assembly?" help="Use the reference annotation file (in GTF or GFF3 format) to guide the assembly process. The output will include expressed reference transcripts as well as any novel transcripts that are assembled. This option is required by option -e (Use Reference transcripts only), see below.">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	122 <option value="yes">Use reference GTF/GFF3</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	123 <option value="no" selected="True" >Do not use reference GTF/GFF3</option>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	124 </param>
62d212192002 Imported from capsule None iuc parents: diff changeset	125 <when value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	126 <when value="yes">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	127 <conditional name="guide_source">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	128 <param name="guide_gff_select" type="select" label="Reference file">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	129 <option value="cached" selected="true">Use a built-in file</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	130 <option value="history">Use a file from history</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	131 </param>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	132 <when value="cached">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	133 <param name="ref_builtin" type="select" label="Use a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	134 <options from_data_table="gene_sets">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	135 <filter type="sort_by" column="2" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	136 <validator type="no_options" message="No GTF file is available." />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	137 </options>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	138 </param>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	139 </when>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	140 <when value="history">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	141 <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	142 </when>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	143 </conditional>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	144 <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="False" label="Use Reference transcripts only?" help="Limit the processing of read alignments to only estimate and output the assembled transcripts matching the reference transcripts given with the -G option. With this option, read bundles with no reference transcripts (novel transcripts) will be entirely skipped, which may provide a considerable speed boost when the given set of reference transcripts is limited to a set of target genes, for example. Default: No"/>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	145 <conditional name="special_outputs">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	146 <param name="special_outputs_select" type="select" label="Output files for differential expression?" help="Select to output additional files that can be used with Ballgown or DESeq2/edgeR. See Help section below for more information">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	147 <option value="ballgown">Ballgown</option>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	148 <option value="deseq2">DESeq2/edgeR</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	149 <option value="no" selected="True">No additional output</option>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	150 </param>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	151 <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	152 <when value="deseq2">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	153 <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75" />
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	154 <param name="clustering" argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" checked="false" label="Cluster overlapping genes" help="Choose whether to cluster genes with different gene IDs that overlap. Transcripts containing the geneID prefix will be ignored. Default: No" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	155 <param argument="--string" type="text" label="Prefix used for transcripts" help="If a different prefix was used for geneIDs assigned by StringTie than the default, specify it here. Only letters and numbers will be retained in this field. Default: MSTRG" >
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	156 <sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	157 <valid initial="string.letters,string.digits"></valid>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	158 </sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	159 </param>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	160 <param argument="--key" type="text" label="Prefix for clustering" help="If clustering, what prefix to use for geneIDs assigned by this script. Only letters and numbers will be retained in this field. Default: prepG">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	161 <sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	162 <valid initial="string.letters,string.digits"></valid>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	163 </sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	164 </param>
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	165 <param name="keep_header" type="boolean" checked="true" label="Output header line?" help="Keep the header line for edgeR, remove it for DESeq2" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	166 </when>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	167 <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	168 </conditional>
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	169 <param name="coverage_file" argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="False" label="Output coverage file?" help="If StringTie is run with this option (requires -G), it returns a file with all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described below. Each line of the GTF is corresponds to a gene or transcript in the reference annotation. Default: No"/>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	170 </when>
62d212192002 Imported from capsule None iuc parents: diff changeset	171 </conditional>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	172 <section name="adv" title="Advanced Options">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	173 <param name="abundance_estimation" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Output gene abundance estimation file?" help="If selected, gene abundances will be reported in a tab-delimited file, see below for more information. Default: No"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	174 <param name="omit_sequences" argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences. This parameter can be a single reference sequence name (e.g. chrM) or a comma-delimited list of sequence names (e.g. chrM,chrX,chrY). This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases, even though they may be of no interest for a particular RNA-Seq analysis. The reference sequence names are case sensitive, they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place." />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	175 <param name="name_prefix" argument="-l" type="text" label="Name prefix for output transcripts" help="This prefix will be added to the name of the transcripts that are output. Only letters and numbers will be retained in this field. Default: STRG">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	176 <sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	177 <valid initial="string.letters,string.digits"></valid>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	178 </sanitizer>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	179 </param>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	180 <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.15" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.15"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	181 <param name="min_tlen" argument="-m" type="integer" min="0" value="200" label="Minimum assembled transcript length" help="Sets the minimum length allowed for the predicted transcripts. Default: 200"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	182 <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	183 <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	184 <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	185 <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	186 <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	187 <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="False" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	188 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Disable multi-mapping correction" help="Default: No"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	189 </section>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	190 </inputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	191 <outputs>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	192 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	193 <data name="gene_abundance_estimation" format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	194 <filter>adv['abundance_estimation']</filter>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	195 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	196 <data name="coverage" format="gtf" label="${tool.name} on ${on_string}: Coverage">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	197 <filter>guide['use_guide'] == 'yes' and guide['coverage_file'] is True </filter>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	198 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	199 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	200 label="${tool.name} on ${on_string}: exon-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	201 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	202 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	203 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	204 label="${tool.name} on ${on_string}: intron-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	205 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	206 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	207 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	208 label="${tool.name} on ${on_string}: transcript-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	209 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	210 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	211 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	212 label="${tool.name} on ${on_string}: exon to transcript mapping">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	213 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	214 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	215 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	216 label="${tool.name} on ${on_string}: intron to transcript mapping">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	217 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	218 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	219 <data name="gene_counts" format="tabular" from_work_dir="special_de_output/sample1/gene_counts.tsv" label="${tool.name} on ${on_string}: Gene counts">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	220 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	221 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	222 <data name="transcript_counts" format="tabular" from_work_dir="special_de_output/sample1/transcript_counts.tsv" label="${tool.name} on ${on_string}: Transcript counts">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	223 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	224 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	225 <data name="legend" format="tabular" from_work_dir="special_de_output/sample1/legend.tsv" label="${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	226 <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	227 </data>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	228 </outputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	229 <tests>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	230 <!--Ensure default GTF output works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	231 <test expect_num_outputs="1">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	232 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	233 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	234 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	235 <!--Ensure fraction option works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	236 <test expect_num_outputs="1">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	237 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	238 <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	239 <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	240 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	241 <!--Ensure guide option works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	242 <test expect_num_outputs="1">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	243 <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	244 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	245 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	246 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	247 <output name="output_gtf" file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	248 </test>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	249 <!--Ensure guide with fraction works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	250 <test expect_num_outputs="1">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	251 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	252 <param name="use_guide" value="yes" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	253 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	254 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	255 <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	256 <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	257 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	258 <!--Ensure coverage and output for Ballgown works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	259 <test expect_num_outputs="7">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	260 <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	261 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	262 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	263 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	264 <param name="special_outputs_select" value="ballgown" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	265 <param name="coverage_file" 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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	272 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
0 62d212192002 Imported from capsule None iuc parents: diff changeset	273 </test>
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	274 <!--Ensure output for edgeR works -->
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	275 <test expect_num_outputs="5">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	276 <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	277 <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	278 <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	279 <param name="input_estimation" value="True" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	280 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	281 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	282 <param name="coverage_file" value="True" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	283 <param name="clustering" value="True" />
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	284 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	285 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	286 <output name="legend" file="legend.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	287 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	288 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	289 </test>
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	290 <!--Ensure output for DESeq2 works -->
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	291 <test expect_num_outputs="5">
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	292 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	293 <param name="use_guide" value="yes" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	294 <param name="special_outputs_select" value="deseq2" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	295 <param name="keep_header" value="False" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	296 <param name="input_estimation" value="True" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	297 <param name="guide_gff_select" value="history" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	298 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	299 <param name="coverage_file" value="True" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	300 <param name="clustering" value="True" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	301 <output name="gene_counts" file="gene_counts_deseq2.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	302 <output name="transcript_counts" file="transcript_counts_deseq2.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	303 <output name="legend" file="legend.tsv" ftype="tabular" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	304 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	305 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	306 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	307 <!--Ensure gene abundances output works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	308 <test expect_num_outputs="2">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	309 <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	310 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	311 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	312 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	313 <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	314 <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	315 <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	316 <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	317 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	318 <!--Ensure another fraction value works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	319 <test expect_num_outputs="1">
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	320 <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	321 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	322 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	323 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	324 <param name="fraction" value="0.15" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	325 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	326 </test>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	327 <!--Ensure built-in GTFs work -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	328 <test expect_num_outputs="1">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	329 <param name="input_bam" ftype="bam" dbkey="hg38" value="stringtie_in1.bam" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	330 <param name="use_guide" value="yes" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	331 <param name="guide_gff_select" value="cached" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	332 <param name="fraction" value="0.15" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	333 <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	334 </test>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	335 </tests>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	336 <help><![CDATA[
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	337
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	338 .. class:: infomark
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	339
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	340 What it does
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	341
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	342 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 of longer sequences that have been assembled from those reads. In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown_, Cuffdiff_ or other programs (DESeq2_, edgeR_, etc.).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	343
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	344 -----
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	345
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	346 Inputs
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	347
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	348 StringTie takes as input a BAM (or SAM) file of paired-end RNA-seq reads, which must be sorted by genomic location (coordinate position). This file contains spliced read alignments and can be produced directly by programs such as HISAT2_. We recommend using HISAT2 as it is a fast and accurate alignment program. Every spliced read alignment (i.e. an alignment across at least one junction) in the input BAM file must contain the tag XS to indicate the genomic strand that produced the RNA from which the read was sequenced. Alignments produced by HISAT2 (when run with --dta option) already include this tag, but if you use a different read mapper you should check that this XS tag is included for spliced alignments.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	349
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	350 NOTE: be sure to run HISAT2 with the --dta option for alignment (under Spliced alignment options), or your results will suffer.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	351
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	352 Also note that if your reads are from a stranded library, you need to choose the appropriate setting under Specify strand information above. As, if Forward (FR) is selected, StringTie will assume the reads are from a --fr library, while if Reverse (RF) is selected, StringTie will assume the reads are from a --rf library, otherwise it is assumed that the reads are from an unstranded library (The widely-used, although now deprecated, TopHat had a similar --library-type option, where fr-firststrand corresponded to RF; fr-secondstrand corresponded to FR). If you don't know whether your reads are from are a stranded library or not, you could use the tool RSeQC Infer Experiment to try to determine.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	353
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	354 As an option, a reference annotation file in `GTF/GFF3`_ format can be provided to StringTie. In this case, StringTie will prefer to use these "known" genes from the annotation file, and for the ones that are expressed it will compute coverage, TPM and FPKM values. It will also produce additional transcripts to account for RNA-seq data that aren't covered by (or explained by) the annotation. Note that if option -e is not used the reference transcripts need to be fully covered by reads in order to be included in StringTie's output. In that case, other transcripts assembled from the data by StringTie and not present in the reference file will be printed as well.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	355
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	356 NOTE: we highly recommend that you provide annotation if you are analyzing a genome that is well-annotated, such as human, mouse, or other model organisms.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	357
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	358 -----
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	359
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	360 Outputs
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	361
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	362 StringTie's primary output is
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	363
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	364 * a GTF file containing the Assembled transcripts
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	365
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	366 Optionally, it can output
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	367
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	368 * a TSV (tab-delimited) file of Gene abundances
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	369
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	370 If a reference GTF/GFF3 file is used as a guide, StringTie can also output:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	371
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	372 * a GTF file containing all fully-covered reference transcripts in the provided reference file that are covered end-to-end by reads
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	373 * Files (tables) for Ballgown and/or DESeq2/edgeR, which can use them to estimate differential expression
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	374
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	375
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	376 StringTie's primary GTF output
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	377
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	378 The primary output of StringTie is a Gene Transfer Format (GTF) file that contains details of the transcripts that StringTie assembles from RNA-Seq data. GTF is an extension of GFF (Gene Finding Format, also called General Feature Format), and is very similar to GFF2 and GFF3. The field definitions for the 9 columns of GTF output can be found at the `Ensembl site here`_. The following is an example of a transcript assembled by StringTie as shown in a GTF file:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	379
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	380 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	381 seqname source feature start end score strand frame attributes
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	382 ----------- ---------- ----------- --------- ------- --------- ---------- --------- -------------------------------------------------------------------------------------------
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	383 chrX StringTie transcript 281394 303355 1000 \+ . gene_id "ERR188044.1"; transcript_id "ERR188044.1.1"; reference_id "NM_018390"; ref_gene_id
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	384 "NM_018390"; ref_gene_name "PLCXD1"; cov "101.256691"; FPKM "530.078918"; TPM "705.667908";
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	385 chrX StringTie exon 281394 281684 1000 \+ . gene_id "ERR188044.1"; transcript_id "ERR188044.1.1"; exon_number "1"; reference_id
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	386 "NM_018390"; ref_gene_id "NM_018390"; ref_gene_name "PLCXD1"; cov "116.270836";
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	387 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	388
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	389
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	390 * seqname: Denotes the chromosome, contig, or scaffold for this transcript. Here the assembled transcript is on chromosome X.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	391
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	392 * source: The source of the GTF file. Since this example was produced by StringTie, this column simply shows 'StringTie'.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	393
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	394 * feature: Feature type (e.g., exon, transcript, mRNA, 5'UTR).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	395
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	396 * start: Start position of the feature (exon, transcript, etc), using a 1-based index.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	397
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	398 * end: End position of the feature, using a 1-based index.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	399
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	400 * score: A confidence score for the assembled transcript. Currently this field is not used, and StringTie reports a constant value of 1000 if the transcript has a connection to a read alignment bundle.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	401
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	402 * strand: If the transcript resides on the forward strand, '+'. If the transcript resides on the reverse strand, '-'.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	403
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	404 * frame: Frame or phase of CDS features. StringTie does not use this field and simply records a ".".
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	405
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	406 * attributes: A semicolon-separated list of tag-value pairs, providing additional information about each feature. Depending on whether an instance is a transcript or an exon and on whether the transcript matches the reference annotation file provided by the user, the content of the attributes field will differ. The following list describes the possible attributes shown in this column:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	407
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	408 * gene_id: A unique identifier for a single gene and its child transcript and exons based on the alignments' file name.
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	409
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	410 * transcript_id: A unique identifier for a single transcript and its child exons based on the alignments' file name.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	411
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	412 * exon_number: A unique identifier for a single exon, starting from 1, within a given transcript.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	413
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	414 * reference_id: The transcript_id in the reference annotation (optional) that the instance matched.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	415
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	416 * ref_gene_id: The gene_id in the reference annotation (optional) that the instance matched.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	417
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	418 * ref_gene_name: The gene_name in the reference annotation (optional) that the instance matched.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	419
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	420 * cov: The average per-base coverage for the transcript or exon.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	421
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	422 * FPKM: Fragments per kilobase of transcript per million read pairs. This is the number of pairs of reads aligning to this feature, normalized by the total number of fragments sequenced (in millions) and the length of the transcript (in kilobases).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	423
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	424 * TPM: Transcripts per million. This is the number of transcripts from this particular gene normalized first by gene length, and then by sequencing depth (in millions) in the sample. A detailed explanation and a comparison of TPM and FPKM can be found here_, and TPM was defined `by B. Li and C. Dewey here`_.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	425
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	426
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	427 Gene abundances in tab-delimited format
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	428
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	429 If StringTie is run with the -A option, it returns a file containing gene abundances. The tab-delimited gene abundances output file has nine fields; below is an example of a gene abundance file produced by StringTie using reference annotation:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	430
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	431 =========== ============= ============= ========== ========= ======= ============ ======== ========
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	432 Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	433 ----------- ------------- ------------- ---------- --------- ------- ------------ -------- --------
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	434 NM_000451 SHOX chrX \+ 624344 646823 0.000000 0.000000 0.000000
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	435 NM_006883 SHOX chrX \+ 624344 659411 0.000000 0.000000 0.000000
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	436 =========== ============= ============= ========== ========= ======= ============ ======== ========
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	437
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	438 * Gene ID: The gene identifier comes from the reference annotation provided with the -G option. If no reference is provided this field is replaced with the name prefix for output transcripts (-l).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	439 * Gene Name: This field contains the gene name in the reference annotation provided with the -G option. If no reference is provided this field is populated with '-'.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	440 * Reference: Name of the reference sequence that was used in the alignment of the reads. Equivalent to the 3rd column in the .SAM alignment.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	441 * Strand: '+' denotes that the gene is on the forward strand, '-' for the reverse strand.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	442 * Start: Start position of the gene (1-based index).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	443 * End: End position of the gene (1-based index).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	444 * Coverage: Per-base coverage of the gene.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	445 * FPKM: normalized expression level in FPKM units (see previous section).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	446 * TPM: normalized expression level in RPM units (see previous section).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	447
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	448 Fully covered transcripts matching the reference annotation transcripts (in GTF format)
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	449
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	450 If StringTie is run with the use reference guide option (-G), it will also return a file with all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	451
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	452 Ballgown Input Table Files
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	453
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	454 An option to output files for Ballgown can be selected under Output additional files above. If selected, StringTie will return Ballgown input table files containing coverage data for the reference transcripts given with the -G option. These tables have these specific names: (1) e2t.ctab, (2) e_data.ctab, (3) i2t.ctab, (4) i_data.ctab, and (5) t_data.ctab. A detailed description of each of these five required inputs to Ballgown can be found at `this link`. With this option StringTie can be used as a direct replacement of the tablemaker program included with the Ballgown distribution.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	455
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	456
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	457 DESeq2/edgeR Input Table Files
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	458
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	459 DESeq2_ and edgeR_ are two popular Bioconductor_ packages for analyzing differential expression, which take as input a matrix of read counts mapped to particular genomic features (e.g., genes). This read count information can be extracted directly from the files generated by StringTie (run with the -e parameter) by selecting DESeq2/edgeR under Output additional files above. This uses the StringTie helper script ``prepDE.py`` to convert the GTF output from StringTie into two tab-delimited (TSV) files, containing the count matrices for genes and transcripts, using the coverage values found in the output of StringTie -e.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	460
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	461 -----
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	462
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	463 More Information
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	464
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	465 Evaluating transcript assemblies:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	466 A simple way of getting more information about the transcripts assembled by StringTie (summary of gene and transcript counts, novel vs. known etc.), or even performing basic tracking of assembled isoforms across multiple RNA-Seq experiments, is to use the gffcompare program. Basic usage information for this program can be found on the `GFF utilities page`_.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	467
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	468 Differential expression analysis:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	469
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	470 Together with HISAT and Ballgown (or DESeq2/edgeR), StringTie can be used for estimating differential expression across multiple RNA-Seq samples and generating plots and differential expression tables as described in our `protocol paper`_ and shown in a diagram in the `StringTie manual here`_.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	471
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	472 Our recommended workflow includes the following steps:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	473
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	474 1. For each RNA-Seq sample, map the reads to the genome with HISAT2 using the --dta option. It is highly recommended to use the reference annotation information when mapping the reads, which can be either embedded in the genome index (built with the --ss and --exon options, see HISAT2 manual), or provided separately at run time (using the --known-splicesite-infile option of HISAT2). The SAM output of each HISAT2 run must be sorted and converted to BAM using samtools as explained above.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	475
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	476 2. For each RNA-Seq sample, use this StringTie tool to assemble the read alignments obtained in the previous step; it is recommended to run StringTie with the -G option if the reference annotation is available.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	477
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	478 3. Run the separate StringTie merge tool in order to generate a non-redundant set of transcripts observed in all the RNA-Seq samples assembled previously. ``StringTie merge`` takes as input a list of all the assembled transcripts files (in GTF format) previously obtained for each sample, as well as a reference annotation file (-G option) if available.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	479
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	480 4. For each RNA-Seq sample, run this StringTie tool selecting to output files for Ballgown (or DESeq2/edgeR), which will generate tables of transcript and gene estimated abundances (count files). The option -e (Use Reference transcripts only) is not required but is recommended for this run in order to produce more accurate abundance estimations of the input transcripts. Each StringTie run in this step will take as input the sorted read alignments (BAM file) obtained in step 1 for the corresponding sample and the -G option with the merged transcripts (GTF file) generated by ``stringtie merge`` in step 3. Please note that this is the only case where the -G option is not used with a reference annotation, but with the global, merged set of transcripts as observed across all samples. (This step is the equivalent of the Tablemaker step described in the original Ballgown pipeline.)
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	481
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	482 5. Ballgown (or DESeq2/edgeR) can now be used to load the coverage tables generated in the previous step and perform various statistical analyses for differential expression, generate plots etc.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	483
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	484 An alternate, faster differential expression analysis workflow can be pursued if there is no interest in novel isoforms (i.e. assembled transcripts present in the samples but missing from the reference annotation), or if only a well known set of transcripts of interest are targeted by the analysis. This simplified protocol has only 3 steps (depicted in the `StringTie manual here`_) as it bypasses the individual assembly of each RNA-Seq sample and the "transcript merge" step. This simplified workflow attempts to directly estimate and analyze the expression of a known set of transcripts as given in the reference annotation file.
0 62d212192002 Imported from capsule None iuc parents: diff changeset	485
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	486 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	487 .. _Ballgown: https://www.biorxiv.org/content/early/2014/09/05/003665
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	488 .. _Cuffdiff: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	489 .. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	490 .. _edgeR: https://bioconductor.org/packages/release/bioc/html/edgeR.html
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	491 .. _Bioconductor: https://www.bioconductor.org/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	492 .. _SAM: http://samtools.github.io/hts-specs/SAMv1.pdf
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	493 .. _HISAT2: http://ccb.jhu.edu/software/hisat2
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	494 .. _`GTF/GFF3`: https://ccb.jhu.edu/software/stringtie/gff.shtml
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	495 .. _`this link`: https://github.com/alyssafrazee/ballgown#ballgown-readable-expression-output
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	496 .. _`Ensembl site here`: http://useast.ensembl.org/info/website/upload/gff.html
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	497 .. _here: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	498 .. _`by B. Li and C. Dewey here`: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	499 .. _`GFF utilities page`: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	500 .. _`protocol paper`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	501 .. _`StringTie manual here`: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	502
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	503 ]]></help>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	504 <expand macro="citations" />
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	505 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 13:a305d75e13f2 draft