stringtie: stringtie.xml annotate

annotate stringtie.xml @ 24:b5a73e1b550b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3"

author	iuc
date	Sat, 25 Sep 2021 18:19:42 +0000
parents	7506ac12fecb
children	93404dcc9c96

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>
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	3 <xrefs>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	4 <xref type="bio.tools">stringtie</xref>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	5 </xrefs>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	6 <macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	7 <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	8 </macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	9 <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	10 <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	11 <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	12 <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	13 #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	14 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	15
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	16 ## 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	17
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	18 #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	19 #if $guide.guide_source.guide_gff_select == "history":
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	20 ln -s '$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	21 #elif $guide.guide_source.guide_gff_select == "cached":
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	22 ln -s '$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	23 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	24 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	25
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	26 #if $input_options.input_mode in ['short_reads','long_reads']:
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	27 #if $input_options.input_bam.metadata.ftype == 'sam':
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	28 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam' -T "\${TMPDIR:-.}" \| stringtie
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	29 #else
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	30 stringtie '$input_options.input_bam'
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	31 #end if
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	32 #if $input_options.input_mode == 'long_reads'
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	33 -L
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	34 -E $input_options.error_splice
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	35 #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	36 #else
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	37 #if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'bam':
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	38 strigtie '$input_options.input_bam_short' '$input_options.input_bam_long'
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	39 #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype == 'bam':
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	40 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	41 && stringtie short_sorted.sam '$input_options.input_bam_long'
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	42 #else if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'sam':
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	43 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	44 && stringtie'$input_options.input_bam_short' long_sorted.sam
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	45 #else
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	46 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	47 && samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	48 && stringtie short_sorted.sam long_sorted.sam
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	49 #end if
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	50 -E $input_options.error_splice
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	51 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	52
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	53 -o '$output_gtf'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	54 -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	55
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	56 $rna_strandness
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	57
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	58 #if str($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	59 -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	60 #if $guide.coverage_file:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	61 -C '$coverage'
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 $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	64 #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	65 -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	66 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	67 #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	68
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	69 #if $adv.name_prefix:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	70 -l '$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	71 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	72 -f '$adv.fraction'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	73 -m '$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	74 -a '$adv.min_anchor_len'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	75 -j '$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	76 -c '$adv.min_bundle_cov'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	77 -g '$adv.bdist'
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	78 -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	79 $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	80 $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	81 #if $adv.abundance_estimation:
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	82 -A '$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	83 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	84 #if str($adv.omit_sequences).strip() != "":
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	85 -x '$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	86 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	87
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	88 #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	89 #if $guide.special_outputs.special_outputs_select == 'deseq2':
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	90 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($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	91 &&
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	92 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	93 &&
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	94 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	95 &&
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	96 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	97 &&
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	98 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	99 -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	100 -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	101 -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	102 -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	103 #if $guide.special_outputs.string:
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	104 -s '$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	105 #end if
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	106 #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	107 -c
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	108 #if $guide.special_outputs.key:
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	109 -k '$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	110 #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	111 --legend '$legend'
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	112 > /dev/null
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	113 &&
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	114 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" '$legend'
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	115 #else
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	116 > /dev/null
0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	117 #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	118
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	119 ## 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	120 &&
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	121 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	122 ## Output header
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	123 &&
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	124 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	125 &&
f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	126 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	127 ## 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	128 &&
20 48258a274be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712 iuc parents: 19 diff changeset	129 tail -n +2 gene_counts.csv \| sort -t"\${TAB}" -k1,1 >> '$gene_counts'
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	130 &&
20 48258a274be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712 iuc parents: 19 diff changeset	131 tail -n +2 transcript_counts.csv \| sort -t"\${TAB}" -k1,1 >> '$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	132 #end if
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	133 #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	134 ]]></command>
5 8836aad67a33 Uploaded iuc parents: diff changeset	135 <inputs>
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	136 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	137 <param name="input_mode" type="select" label="Input options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	138 <option value="short_reads">Short reads</option>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	139 <option value="long_reads">Long reads</option>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	140 <option value="mixed_reads">Mixed mode: short and long reads</option>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	141 </param>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	142 <when value="short_reads">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	143 <param name="input_bam" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	144 </when>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	145 <when value="long_reads">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	146 <param name="input_bam" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	147 <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	148 </when>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	149 <when value="mixed_reads">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	150 <param name="input_bam_short" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	151 <param name="input_bam_long" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	152 <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	153 </when>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	154 </conditional>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	155 <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	156 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	157 <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	158 <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	159 <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	160 </param>
5 8836aad67a33 Uploaded iuc parents: diff changeset	161 <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	162 <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	163 <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	164 <option value="no" selected="true" >Do not use reference GTF/GFF3</option>
5 8836aad67a33 Uploaded iuc parents: diff changeset	165 </param>
8836aad67a33 Uploaded iuc parents: diff changeset	166 <when value="no" />
8836aad67a33 Uploaded iuc parents: diff changeset	167 <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	168 <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	169 <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	170 <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	171 <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	172 </param>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	173 <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	174 <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	175 <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	176 <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	177 <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	178 </options>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	179 </param>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	180 </when>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	181 <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	182 <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	183 </when>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	184 </conditional>
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="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	186 <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	187 <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	188 <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	189 <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	190 <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	191 </param>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	192 <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	193 <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	194 <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	195 <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	196 <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	197 <sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	198 <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	199 </sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	200 </param>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	201 <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	202 <sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	203 <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	204 </sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	205 </param>
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	206 </when>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	207 <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	208 </conditional>
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	209 <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	210 </when>
8836aad67a33 Uploaded iuc parents: diff changeset	211 </conditional>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	212 <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	213 <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	214 <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	215 <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	216 <sanitizer>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	217 <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	218 </sanitizer>
5 8836aad67a33 Uploaded iuc parents: diff changeset	219 </param>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	220 <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	221 <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	222 <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	223 <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	224 <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	225 <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	226 <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	227 <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	228 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	229 <param name="point_features" type="data" format="tabular" optional="True" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	230 </section>
5 8836aad67a33 Uploaded iuc parents: diff changeset	231 </inputs>
8836aad67a33 Uploaded iuc parents: diff changeset	232 <outputs>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	233 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
22 ed3da12f8c37 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 21 diff changeset	234 <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates">
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	235 <filter>adv['abundance_estimation']</filter>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	236 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	237 <data name="coverage" format="gtf" label="${tool.name} on ${on_string}: Coverage">
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	238 <filter>guide['use_guide'] == 'yes' and guide['coverage_file'] is True </filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	239 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	240 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	241 label="${tool.name} on ${on_string}: exon-level expression measurements">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	242 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	243 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	244 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	245 label="${tool.name} on ${on_string}: intron-level expression measurements">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	246 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	247 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	248 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	249 label="${tool.name} on ${on_string}: transcript-level expression measurements">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	250 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	251 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	252 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	253 label="${tool.name} on ${on_string}: exon to transcript mapping">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	254 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	255 </data>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	256 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	257 label="${tool.name} on ${on_string}: intron to transcript mapping">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	258 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	259 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	260 <data name="gene_counts" format="tabular" from_work_dir="special_de_output/sample1/gene_counts.tsv" label="${tool.name} on ${on_string}: Gene counts">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	261 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
5 8836aad67a33 Uploaded iuc parents: diff changeset	262 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	263 <data name="transcript_counts" format="tabular" from_work_dir="special_de_output/sample1/transcript_counts.tsv" label="${tool.name} on ${on_string}: Transcript counts">
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	264 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	265 </data>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	266 <data name="legend" format="tabular" from_work_dir="special_de_output/sample1/legend.tsv" label="${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	267 <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	268 </data>
8836aad67a33 Uploaded iuc parents: diff changeset	269 </outputs>
8836aad67a33 Uploaded iuc parents: diff changeset	270 <tests>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	271 <!--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	272 <test expect_num_outputs="1">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	273 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	274 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	275 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	276 </conditional>
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	277 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="4" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	278 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	279 <!--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	280 <test expect_num_outputs="1">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	281 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	282 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	283 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	284 </conditional>
5 8836aad67a33 Uploaded iuc parents: diff changeset	285 <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	286 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="4" />
5 8836aad67a33 Uploaded iuc parents: 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 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	289 <test expect_num_outputs="1">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	290 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	291 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	292 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	293 </conditional>
5 8836aad67a33 Uploaded iuc parents: diff changeset	294 <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	295 <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	296 <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	297 <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	298 </test>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	299 <!--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	300 <test expect_num_outputs="1">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	301 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	302 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	303 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	304 </conditional>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	305 <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	306 <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	307 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	308 <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	309 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="4" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	310 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	311 <!--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	312 <test expect_num_outputs="7">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	313 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	314 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	315 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	316 </conditional>
5 8836aad67a33 Uploaded iuc parents: diff changeset	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" />
5 8836aad67a33 Uploaded iuc parents: diff changeset	329 </test>
19 0c85a528a771 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 17 diff changeset	330 <!--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	331 <test expect_num_outputs="5">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	332 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	333 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	334 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	335 </conditional>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	336 <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	337 <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	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 <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	345 <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	346 <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	347 <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	348 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	349 <!--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	350 <test expect_num_outputs="2">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	351 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	352 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	353 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	354 </conditional>
15 457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 12 diff changeset	355 <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	356 <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	357 <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	358 <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	359 <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	360 <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	361 <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	362 </test>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	363 <!--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	364 <test expect_num_outputs="1">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	365 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	366 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	367 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	368 </conditional>
10 ce5e12ebb972 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 9 diff changeset	369 <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	370 <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	371 <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	372 <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	373 <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	374 </test>
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	375 <!--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	376 <test expect_num_outputs="1">
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	377 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	378 <param name="input_mode" value="short_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	379 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	380 </conditional>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	381 <param name="use_guide" value="yes" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	382 <param name="guide_gff_select" value="cached" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	383 <param name="fraction" value="0.15" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	384 <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	385 </test>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	386 <!-- Test long reads input -->
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	387 <test expect_num_outputs="1">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	388 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	389 <param name="input_mode" value="long_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	390 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	391 </conditional>
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	392 <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	393 <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	394 <param name="fraction" value="0.15" />
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	395 <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	396 </test>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	397 <!-- Test error splice option -->
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	398 <test expect_num_outputs="1">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	399 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	400 <param name="input_mode" value="long_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	401 <param name="input_bam" ftype="bam" value="long_reads.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	402 <param name="error_splice" value="30" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	403 </conditional>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	404 <param name="use_guide" value="yes" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	405 <param name="guide_gff_select" value="cached" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	406 <param name="fraction" value="0.15" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	407 <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	408 </test>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	409 <!-- Test mixed reads input -->
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	410 <test expect_num_outputs="1">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	411 <conditional name="input_options">
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	412 <param name="input_mode" value="mixed_reads"/>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	413 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	414 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	415 </conditional>
b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	416 <output name="output_gtf" file="stringtie_out12.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	417 </test>
5 8836aad67a33 Uploaded iuc parents: diff changeset	418 </tests>
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	419 <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	420
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	421 .. class:: infomark
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	422
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	423 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	424
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	425 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	426
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	427 -----
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 Inputs
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 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	432
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	433 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	434
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	435 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	436
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	437 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	438
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	439 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	440
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 Outputs
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	444
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	445 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	446
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	447 * 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	448
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	449 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	450
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	451 * 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	452
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	453 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	454
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	455 * 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	456 * 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	457
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 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	460
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	461 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	462
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	463 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	464 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	465 ----------- ---------- ----------- --------- ------- --------- ---------- --------- -------------------------------------------------------------------------------------------
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	466 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	467 "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	468 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	469 "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	470 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	471
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	472
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	473 * 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	474
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	475 * 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	476
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	477 * 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	478
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	479 * 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	480
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	481 * 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	482
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	483 * 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	484
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	485 * 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	486
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	487 * 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	488
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	489 * 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	490
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	491 * 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	492
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	493 * 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	494
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	495 * 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	496
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	497 * 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	498
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	499 * 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	500
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	501 * 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	502
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	503 * 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	504
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	505 * 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	506
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	507 * 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	508
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	509
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	510 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	511
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	512 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	513
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	514 =========== ============= ============= ========== ========= ======= ============ ======== ========
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	515 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	516 ----------- ------------- ------------- ---------- --------- ------- ------------ -------- --------
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	517 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	518 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	519 =========== ============= ============= ========== ========= ======= ============ ======== ========
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	520
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	521 * 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	522 * 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	523 * 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	524 * 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	525 * 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	526 * 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	527 * 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	528 * 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	529 * 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	530
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	531 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	532
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	533 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	534
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	535 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	536
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	537 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	538
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	539
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	540 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	541
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	542 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	543
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	544 -----
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	545
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	546 More Information
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	547
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	548 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	549 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	550
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	551 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	552
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	553 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	554
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	555 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	556
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	557 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	558
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	559 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	560
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	561 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	562
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	563 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	564
21 f4e465352f50 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 20 diff changeset	565 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	566
d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	567 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	568
8 6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389 iuc parents: 5 diff changeset	569 .. _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	570 .. _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	571 .. _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	572 .. _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	573 .. _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	574 .. _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	575 .. _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	576 .. _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	577 .. _HISAT2: http://ccb.jhu.edu/software/hisat2
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	578 .. _`GTF/GFF3`: http://ccb.jhu.edu/software/stringtie/gff.shtml
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	579 .. _`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	580 .. _`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	581 .. _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	582 .. _`by B. Li and C. Dewey here`: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	583 .. _`GFF utilities page`: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	584 .. _`protocol paper`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/
24 b5a73e1b550b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 23 diff changeset	585 .. _`StringTie manual here`: http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
17 d2d010512422 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 64d444baf673f381b5c9e000092d0ef48a543cc4 iuc parents: 16 diff changeset	586
16 bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 15 diff changeset	587 ]]></help>
12 f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0 iuc parents: 11 diff changeset	588 <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	589 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 24:b5a73e1b550b draft