stringtie: stringtie.xml annotate

annotate stringtie.xml @ 22:ed3da12f8c37 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78

author	iuc
date	Fri, 03 May 2019 11:04:29 -0400
parents	f4e465352f50
children	7506ac12fecb

rev	line source
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	1 <tool id="stringtie" name="StringTie" version="@TOOL_VERSION@">
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	2 <description>transcript assembly and quantification</description>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	3 <macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	4 <import>macros.xml</import>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	5 </macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	6 <expand macro="requirements" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	7 <expand macro="stdio" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	8 <expand macro="version_command" />
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	9 <command><![CDATA[
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	10 #import re
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	11 mkdir -p ./special_de_output/sample1/ &&
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	12
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	13 ## Get Guide GTF/GFF if selected
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	14
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	15 #if str($guide.use_guide) == 'yes':
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	16 #if $guide.guide_source.guide_gff_select == "history":
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	17 ln -s '$guide.guide_source.ref_hist' guide.gff &&
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	18 #elif $guide.guide_source.guide_gff_select == "cached":
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	19 ln -s '$guide.guide_source.ref_builtin.fields.path' guide.gff &&
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	20 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	21 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	22
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	23 #if $input_bam.metadata.ftype == 'sam':
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	24 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' \| stringtie
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	25 #else
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	26 stringtie '$input_bam'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	27 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	28
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	29 -o '$output_gtf'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	30 -p "\${GALAXY_SLOTS:-1}"
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	31
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	32 $rna_strandness
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	33
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	34 #if str($guide.use_guide) == 'yes':
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	35 -G guide.gff
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	36 #if $guide.coverage_file:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	37 -C '$coverage'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	38 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	39 $guide.input_estimation
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	40 #if $guide.special_outputs != 'no':
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	41 -b ./special_de_output/sample1/
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	42 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	43 #end if
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	44
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	45 #if $adv.name_prefix:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	46 -l '$adv.name_prefix'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	47 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	48 -f '$adv.fraction'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	49 -m '$adv.min_tlen'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	50 -a '$adv.min_anchor_len'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	51 -j '$adv.min_anchor_cov'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	52 -c '$adv.min_bundle_cov'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	53 -g '$adv.bdist'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	54 -M '$adv.bundle_fraction'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	55 $adv.disable_trimming
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	56 $adv.multi_mapping
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	57 #if $adv.abundance_estimation:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	58 -A '$gene_abundance_estimation'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	59 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	60 #if str($adv.omit_sequences).strip() != "":
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	61 -x '$adv.omit_sequences'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	62 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	63
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	64 #if str($guide.use_guide) == 'yes':
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	65 #if $guide.special_outputs.special_outputs_select == 'deseq2':
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	66 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	67 &&
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	68 ln -s '$output_gtf' ./special_de_output/sample1/output.gtf
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	69 &&
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	70 TAB=\$(printf '\t')
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	71 &&
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	72 CR=\$(printf '\r')
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	73 &&
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	74 prepDE.py
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	75 -i ./special_de_output/
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	76 -g gene_counts.csv
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	77 -t transcript_counts.csv
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	78 -l $guide.special_outputs.read_length
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	79 #if $guide.special_outputs.string:
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	80 -s '$guide.special_outputs.string'
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	81 #end if
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	82 #if $guide.special_outputs.clustering:
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	83 -c
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	84 #if $guide.special_outputs.key:
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	85 -k '$guide.special_outputs.key'
11 52f55ad3dee2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 46636ba3d63d34e9ee30a2e0ee28cca0213628c8 iuc parents: 10 diff changeset	86 #end if
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	87 --legend '$legend'
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	88 > /dev/null
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	89 &&
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	90 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" '$legend'
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	91 #else
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	92 > /dev/null
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	93 #end if
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	94
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	95 ## Replace commas with tabs
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	96 &&
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	97 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" gene_counts.csv transcript_counts.csv
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	98 ## Output header
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	99 &&
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	100 head -n 1 gene_counts.csv \| sed -e 's/sample1/$escaped_element_identifier/' > '$gene_counts'
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	101 &&
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	102 head -n 1 transcript_counts.csv \| sed -e 's/sample1/$escaped_element_identifier/' > '$transcript_counts'
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	103 ## Sort count files on the first column
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	104 &&
20 48258a274be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712 iuc parents: 19 diff changeset	105 tail -n +2 gene_counts.csv \| sort -t"\${TAB}" -k1,1 >> '$gene_counts'
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	106 &&
20 48258a274be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712 iuc parents: 19 diff changeset	107 tail -n +2 transcript_counts.csv \| sort -t"\${TAB}" -k1,1 >> '$transcript_counts'
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	108 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	109 #end if
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	110 ]]></command>
5 8836aad67a33 Uploaded iuc parents: diff changeset	111 <inputs>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	112 <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"/>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	113 <param name="rna_strandness" type="select" label="Specify strand information"
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	114 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">
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	115 <option value="" selected="true">Unstranded</option>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	116 <option value="--fr">Forward (FR)</option>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	117 <option value="--rf">Reverse (RF)</option>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	118 </param>
5 8836aad67a33 Uploaded iuc parents: diff changeset	119 <conditional name="guide">
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	120 <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.">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	121 <option value="yes">Use reference GTF/GFF3</option>
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	122 <option value="no" selected="true" >Do not use reference GTF/GFF3</option>
5 8836aad67a33 Uploaded iuc parents: diff changeset	123 </param>
8836aad67a33 Uploaded iuc parents: diff changeset	124 <when value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	125 <when value="yes">
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	126 <conditional name="guide_source">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	127 <param name="guide_gff_select" type="select" label="Reference file">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	128 <option value="cached" selected="true">Use a built-in file</option>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	129 <option value="history">Use a file from history</option>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	130 </param>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	131 <when value="cached">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	132 <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">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	133 <options from_data_table="gene_sets">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	134 <filter type="sort_by" column="2" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	135 <validator type="no_options" message="No GTF file is available." />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	136 </options>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	137 </param>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	138 </when>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	139 <when value="history">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	140 <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	141 </when>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	142 </conditional>
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	143 <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"/>
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	144 <conditional name="special_outputs">
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	145 <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">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	146 <option value="ballgown">Ballgown</option>
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	147 <option value="deseq2">DESeq2/edgeR/limma-voom</option>
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	148 <option value="no" selected="true">No additional output</option>
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	149 </param>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	150 <when value="ballgown" />
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	151 <when value="deseq2">
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	152 <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75" />
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	153 <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" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	154 <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" >
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	155 <sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	156 <valid initial="string.letters,string.digits"></valid>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	157 </sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	158 </param>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	159 <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">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	160 <sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	161 <valid initial="string.letters,string.digits"></valid>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	162 </sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	163 </param>
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	164 </when>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	165 <when value="no" />
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	166 </conditional>
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	167 <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 corresponds to a gene or transcript in the reference annotation."/>
5 8836aad67a33 Uploaded iuc parents: diff changeset	168 </when>
8836aad67a33 Uploaded iuc parents: diff changeset	169 </conditional>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	170 <section name="adv" title="Advanced Options">
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	171 <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"/>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	172 <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." />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	173 <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">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	174 <sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	175 <valid initial="string.letters,string.digits"></valid>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	176 </sanitizer>
5 8836aad67a33 Uploaded iuc parents: diff changeset	177 </param>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	178 <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"/>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	179 <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"/>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	180 <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" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	181 <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" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	182 <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"/>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	183 <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)"/>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	184 <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"/>
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	185 <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" />
ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	186 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	187 </section>
5 8836aad67a33 Uploaded iuc parents: diff changeset	188 </inputs>
8836aad67a33 Uploaded iuc parents: diff changeset	189 <outputs>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	190 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	191 <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates">
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	192 <filter>adv['abundance_estimation']</filter>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	193 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	194 <data name="coverage" format="gtf" label="${tool.name} on ${on_string}: Coverage">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	195 <filter>guide['use_guide'] == 'yes' and guide['coverage_file'] is True </filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	196 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	197 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	198 label="${tool.name} on ${on_string}: exon-level expression measurements">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	199 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	200 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	201 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	202 label="${tool.name} on ${on_string}: intron-level expression measurements">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	203 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	204 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	205 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	206 label="${tool.name} on ${on_string}: transcript-level expression measurements">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	207 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	208 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	209 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	210 label="${tool.name} on ${on_string}: exon to transcript mapping">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	211 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	212 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	213 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	214 label="${tool.name} on ${on_string}: intron to transcript mapping">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	215 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	216 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	217 <data name="gene_counts" format="tabular" from_work_dir="special_de_output/sample1/gene_counts.tsv" label="${tool.name} on ${on_string}: Gene counts">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	218 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	219 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	220 <data name="transcript_counts" format="tabular" from_work_dir="special_de_output/sample1/transcript_counts.tsv" label="${tool.name} on ${on_string}: Transcript counts">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	221 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	222 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	223 <data name="legend" format="tabular" from_work_dir="special_de_output/sample1/legend.tsv" label="${tool.name} on ${on_string}: legend">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	224 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	225 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	226 </outputs>
8836aad67a33 Uploaded iuc parents: diff changeset	227 <tests>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	228 <!--Ensure default GTF output works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	229 <test expect_num_outputs="1">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	230 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	231 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="4" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	232 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	233 <!--Ensure fraction option works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	234 <test expect_num_outputs="1">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	235 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	236 <param name="fraction" value="0.17" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	237 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	238 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	239 <!--Ensure guide option works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	240 <test expect_num_outputs="1">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	241 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	242 <param name="use_guide" value="yes" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	243 <param name="guide_gff_select" value="history" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	244 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	245 <output name="output_gtf" file="stringtie_out3.gtf" ftype="gtf" lines_diff="4" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	246 </test>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	247 <!--Ensure guide with fraction works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	248 <test expect_num_outputs="1">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	249 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	250 <param name="use_guide" value="yes" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	251 <param name="guide_gff_select" value="history" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	252 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	253 <param name="fraction" value="0.17" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	254 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	255 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	256 <!--Ensure coverage and output for Ballgown works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	257 <test expect_num_outputs="7">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	258 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	259 <param name="use_guide" value="yes" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	260 <param name="guide_gff_select" value="history" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	261 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	262 <param name="special_outputs_select" value="ballgown" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	263 <param name="coverage_file" value="true" />
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	264 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	265 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	266 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	267 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	268 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	269 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="4" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	270 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	271 </test>
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	272 <!--Ensure output for edgeR works -->
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	273 <test expect_num_outputs="5">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	274 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	275 <param name="use_guide" value="yes" />
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	276 <param name="special_outputs_select" value="deseq2" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	277 <param name="input_estimation" value="true" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	278 <param name="guide_gff_select" value="history" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	279 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	280 <param name="coverage_file" value="true" />
ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	281 <param name="clustering" value="true" />
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	282 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	283 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	284 <output name="legend" file="legend.tsv" ftype="tabular" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	285 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="4" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	286 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	287 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	288 <!--Ensure gene abundances output works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	289 <test expect_num_outputs="2">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	290 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	291 <param name="use_guide" value="yes" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	292 <param name="guide_gff_select" value="history" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	293 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	294 <param name="fraction" value="0.17" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	295 <param name="abundance_estimation" value="true" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	296 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	297 <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	298 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	299 <!--Ensure another fraction value works -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	300 <test expect_num_outputs="1">
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	301 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	302 <param name="use_guide" value="yes" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	303 <param name="guide_gff_select" value="history" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	304 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	305 <param name="fraction" value="0.15" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	306 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" />
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	307 </test>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	308 <!--Ensure built-in GTFs work -->
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	309 <test expect_num_outputs="1">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	310 <param name="input_bam" ftype="bam" dbkey="hg38" value="stringtie_in1.bam" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	311 <param name="use_guide" value="yes" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	312 <param name="guide_gff_select" value="cached" />
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	313 <param name="fraction" value="0.15" />
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	314 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" />
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	315 </test>
5 8836aad67a33 Uploaded iuc parents: diff changeset	316 </tests>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	317 <help><![CDATA[
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	318
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	319 .. class:: infomark
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	320
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	321 What it does
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	322
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	323 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_, limma_ etc.).
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	324
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	325 -----
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	326
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	327 Inputs
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	328
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	329 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	330
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	331 NOTE: be sure to run HISAT2 with the --dta option for alignment (under Spliced alignment options), or your results will suffer.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	332
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	333 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	334
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	335 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	336
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	337 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	338
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	339 -----
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	340
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	341 Outputs
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	342
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	343 StringTie's primary output is
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	344
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	345 * a GTF file containing the Assembled transcripts
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	346
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	347 Optionally, it can output
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	348
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	349 * a TSV (tab-delimited) file of Gene abundances
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	350
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	351 If a reference GTF/GFF3 file is used as a guide, StringTie can also output:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	352
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	353 * a GTF file containing all fully-covered reference transcripts in the provided reference file that are covered end-to-end by reads
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	354 * Files (tables) for Ballgown and/or DESeq2/edgeR/limma-voom, which can use them to estimate differential expression
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	355
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	356
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	357 StringTie's primary GTF output
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	358
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	359 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:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	360
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	361 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	362 seqname source feature start end score strand frame attributes
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	363 ----------- ---------- ----------- --------- ------- --------- ---------- --------- -------------------------------------------------------------------------------------------
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	364 chrX StringTie transcript 281394 303355 1000 \+ . gene_id "ERR188044.1"; transcript_id "ERR188044.1.1"; reference_id "NM_018390"; ref_gene_id
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	365 "NM_018390"; ref_gene_name "PLCXD1"; cov "101.256691"; FPKM "530.078918"; TPM "705.667908";
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	366 chrX StringTie exon 281394 281684 1000 \+ . gene_id "ERR188044.1"; transcript_id "ERR188044.1.1"; exon_number "1"; reference_id
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	367 "NM_018390"; ref_gene_id "NM_018390"; ref_gene_name "PLCXD1"; cov "116.270836";
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	368 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	369
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	370
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	371 * seqname: Denotes the chromosome, contig, or scaffold for this transcript. Here the assembled transcript is on chromosome X.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	372
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	373 * source: The source of the GTF file. Since this example was produced by StringTie, this column simply shows 'StringTie'.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	374
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	375 * feature: Feature type (e.g., exon, transcript, mRNA, 5'UTR).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	376
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	377 * start: Start position of the feature (exon, transcript, etc), using a 1-based index.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	378
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	379 * end: End position of the feature, using a 1-based index.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	380
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	381 * 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	382
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	383 * strand: If the transcript resides on the forward strand, '+'. If the transcript resides on the reverse strand, '-'.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	384
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	385 * frame: Frame or phase of CDS features. StringTie does not use this field and simply records a ".".
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	386
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	387 * 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:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	388
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	389 * gene_id: A unique identifier for a single gene and its child transcript and exons based on the alignments' file name.
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	390
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	391 * transcript_id: A unique identifier for a single transcript and its child exons based on the alignments' file name.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	392
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	393 * exon_number: A unique identifier for a single exon, starting from 1, within a given transcript.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	394
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	395 * reference_id: The transcript_id in the reference annotation (optional) that the instance matched.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	396
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	397 * ref_gene_id: The gene_id in the reference annotation (optional) that the instance matched.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	398
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	399 * ref_gene_name: The gene_name in the reference annotation (optional) that the instance matched.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	400
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	401 * cov: The average per-base coverage for the transcript or exon.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	402
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	403 * 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).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	404
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	405 * 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`_.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	406
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	407
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	408 Gene abundances in tab-delimited format
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	409
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	410 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:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	411
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	412 =========== ============= ============= ========== ========= ======= ============ ======== ========
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	413 Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	414 ----------- ------------- ------------- ---------- --------- ------- ------------ -------- --------
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	415 NM_000451 SHOX chrX \+ 624344 646823 0.000000 0.000000 0.000000
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	416 NM_006883 SHOX chrX \+ 624344 659411 0.000000 0.000000 0.000000
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	417 =========== ============= ============= ========== ========= ======= ============ ======== ========
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	418
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	419 * 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).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	420 * 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 '-'.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	421 * Reference: Name of the reference sequence that was used in the alignment of the reads. Equivalent to the 3rd column in the .SAM alignment.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	422 * Strand: '+' denotes that the gene is on the forward strand, '-' for the reverse strand.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	423 * Start: Start position of the gene (1-based index).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	424 * End: End position of the gene (1-based index).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	425 * Coverage: Per-base coverage of the gene.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	426 * FPKM: normalized expression level in FPKM units (see previous section).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	427 * TPM: normalized expression level in RPM units (see previous section).
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	428
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	429 Fully covered transcripts matching the reference annotation transcripts (in GTF format)
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	430
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	431 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	432
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	433 Ballgown Input Table Files
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	434
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	435 An option to output files for Ballgown can be selected under Output files for differential expression? 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.
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	436
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	437
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	438 DESeq2/edgeR/limma-voom Input Table Files
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	439
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	440 DESeq2_, edgeR_ and limma_ are three 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/limma-voom under Output files for differential expression? 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.
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	441
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	442 -----
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	443
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	444 More Information
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	445
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	446 Evaluating transcript assemblies:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	447 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`_.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	448
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	449 Differential expression analysis:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	450
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	451 Together with HISAT and Ballgown (or DESeq2/edgeR/limma-voom), 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`_.
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	452
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	453 Our recommended workflow includes the following steps:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	454
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	455 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	456
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	457 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	458
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	459 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.
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	460
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	461 4. For each RNA-Seq sample, run this StringTie tool selecting to output files for Ballgown (or DESeq2/edgeR/limma-voom), 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.)
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	462
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	463 5. Ballgown (or DESeq2/edgeR/limma-voom) 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.
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	464
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	465 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.
5 8836aad67a33 Uploaded iuc parents: diff changeset	466
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	467 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	468 .. _Ballgown: https://www.biorxiv.org/content/early/2014/09/05/003665
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	469 .. _Cuffdiff: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	470 .. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	471 .. _edgeR: https://bioconductor.org/packages/release/bioc/html/edgeR.html
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	472 .. _limma: https://bioconductor.org/packages/release/bioc/html/limma.html
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	473 .. _Bioconductor: https://www.bioconductor.org/
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	474 .. _SAM: http://samtools.github.io/hts-specs/SAMv1.pdf
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	475 .. _HISAT2: http://ccb.jhu.edu/software/hisat2
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	476 .. _`GTF/GFF3`: https://ccb.jhu.edu/software/stringtie/gff.shtml
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	477 .. _`this link`: https://github.com/alyssafrazee/ballgown#ballgown-readable-expression-output
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	478 .. _`Ensembl site here`: http://useast.ensembl.org/info/website/upload/gff.html
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	479 .. _here: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	480 .. _`by B. Li and C. Dewey here`: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	481 .. _`GFF utilities page`: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	482 .. _`protocol paper`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	483 .. _`StringTie manual here`: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	484
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	485 ]]></help>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	486 <expand macro="citations" />
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	487 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 22:ed3da12f8c37 draft