stringtie: stringtie.xml annotate

annotate stringtie.xml @ 20:cef79931dda5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb

author	iuc
date	Wed, 27 Jul 2022 09:28:15 +0000
parents	333a6e13b622
children	914cfcba0ec8

rev	line source
19 333a6e13b622 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938" iuc parents: 18 diff changeset	1 <tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	2 <description>transcript assembly and quantification</description>
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	3 <xrefs>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	4 <xref type="bio.tools">stringtie</xref>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	5 </xrefs>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	6 <macros>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	7 <import>macros.xml</import>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	8 </macros>
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	9 <expand macro="requirements" />
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	10 <expand macro="stdio" />
d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	11 <expand macro="version_command" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	12 <command><![CDATA[
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	13 #import re
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	14 mkdir -p ./special_de_output/sample1/ &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	15
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	16 ## Get Guide GTF/GFF if selected
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	17
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	18 #if str($guide.use_guide) == 'yes':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	19 #if $guide.guide_source.guide_gff_select == "history":
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	20 ln -s '$guide.guide_source.ref_hist' guide.gff &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	21 #elif $guide.guide_source.guide_gff_select == "cached":
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	22 ln -s '$guide.guide_source.ref_builtin.fields.path' guide.gff &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	23 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	24 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	25
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	26 #if $input_options.input_mode in ['short_reads','long_reads']:
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	27 #if $input_options.input_bam.metadata.ftype == 'sam':
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	28 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam' -T "\${TMPDIR:-.}" \| stringtie
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	29 #else
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	30 stringtie '$input_options.input_bam'
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	31 #end if
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	32 #if $input_options.input_mode == 'long_reads'
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	33 -L
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	34 -E $input_options.error_splice
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	35 #end if
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	36 #else
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	37 #if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'bam':
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	38 strigtie '$input_options.input_bam_short' '$input_options.input_bam_long'
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	39 #else if $input_options.input_bam_short.metadata.ftype == 'sam' and $input_options.input_bam_long.metadata.ftype == 'bam':
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	40 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	41 && stringtie short_sorted.sam '$input_options.input_bam_long'
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	42 #else if $input_options.input_bam_short.metadata.ftype == 'bam' and $input_options.input_bam_long.metadata.ftype == 'sam':
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	43 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	44 && stringtie'$input_options.input_bam_short' long_sorted.sam
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	45 #else
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	46 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_short' -T "\${TMPDIR:-.}" -o short_sorted.sam
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	47 && samtools sort -@ \${GALAXY_SLOTS:-1} '$input_options.input_bam_long' -T "\${TMPDIR:-.}" -o long_sorted.sam
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	48 && stringtie short_sorted.sam long_sorted.sam
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	49 #end if
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	50 -E $input_options.error_splice
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	51 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	52
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	53 -o '$output_gtf'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	54 -p "\${GALAXY_SLOTS:-1}"
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	55
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	56 $rna_strandness
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	57
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	58 #if str($guide.use_guide) == 'yes':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	59 -G guide.gff
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	60 #if $guide.coverage_file:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	61 -C '$coverage'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	62 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	63 $guide.input_estimation
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	64 #if $guide.special_outputs != 'no':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	65 -b ./special_de_output/sample1/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	66 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	67 #end if
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	68
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	69 #if $adv.name_prefix:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	70 -l '$adv.name_prefix'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	71 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	72 -f '$adv.fraction'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	73 -m '$adv.min_tlen'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	74 -a '$adv.min_anchor_len'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	75 -j '$adv.min_anchor_cov'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	76 -c '$adv.min_bundle_cov'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	77 -g '$adv.bdist'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	78 -M '$adv.bundle_fraction'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	79 $adv.disable_trimming
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	80 $adv.multi_mapping
19 333a6e13b622 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938" iuc parents: 18 diff changeset	81 #if $adv.point_features
333a6e13b622 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938" iuc parents: 18 diff changeset	82 --ptf $adv.point_features
333a6e13b622 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938" iuc parents: 18 diff changeset	83 #end if
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	84 #if $adv.abundance_estimation:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	85 -A '$gene_abundance_estimation'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	86 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	87 #if str($adv.omit_sequences).strip() != "":
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	88 -x '$adv.omit_sequences'
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	89 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	90
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	91 #if str($guide.use_guide) == 'yes':
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	92 #if $guide.special_outputs.special_outputs_select == 'deseq2':
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	93 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	94 &&
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	95 ln -s '$output_gtf' ./special_de_output/sample1/output.gtf
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	96 &&
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	97 TAB=\$(printf '\t')
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	98 &&
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	99 CR=\$(printf '\r')
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	100 &&
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	101 prepDE.py
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	102 -i ./special_de_output/
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	103 -g gene_counts.csv
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	104 -t transcript_counts.csv
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	105 -l $guide.special_outputs.read_length
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	106 #if $guide.special_outputs.string:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	107 -s '$guide.special_outputs.string'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	108 #end if
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	109 #if $guide.special_outputs.clustering:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	110 -c
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	111 #if $guide.special_outputs.key:
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	112 -k '$guide.special_outputs.key'
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	113 #end if
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	114 --legend '$legend'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	115 > /dev/null
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	116 &&
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	117 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" '$legend'
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	118 #else
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	119 > /dev/null
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	120 #end if
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	121
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	122 ## Replace commas with tabs
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	123 &&
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	124 sed -i.bak -e "s/,/\${TAB}/g" -e "s/\${CR}//g" gene_counts.csv transcript_counts.csv
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	125 ## Output header
dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	126 &&
dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	127 head -n 1 gene_counts.csv \| sed -e 's/sample1/$escaped_element_identifier/' > '$gene_counts'
dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	128 &&
dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	129 head -n 1 transcript_counts.csv \| sed -e 's/sample1/$escaped_element_identifier/' > '$transcript_counts'
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	130 ## Sort count files on the first column
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	131 &&
14 eafd5dc95228 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712 iuc parents: 13 diff changeset	132 tail -n +2 gene_counts.csv \| sort -t"\${TAB}" -k1,1 >> '$gene_counts'
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	133 &&
14 eafd5dc95228 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 57441e46de7ca04f25df6e43152dc210d4b32712 iuc parents: 13 diff changeset	134 tail -n +2 transcript_counts.csv \| sort -t"\${TAB}" -k1,1 >> '$transcript_counts'
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	135 #end if
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	136 #end if
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	137 ]]></command>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	138 <inputs>
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	139 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	140 <param name="input_mode" type="select" label="Input options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	141 <option value="short_reads">Short reads</option>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	142 <option value="long_reads">Long reads</option>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	143 <option value="mixed_reads">Mixed mode: short and long reads</option>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	144 </param>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	145 <when value="short_reads">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	146 <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"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	147 </when>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	148 <when value="long_reads">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	149 <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"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	150 <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" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	151 </when>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	152 <when value="mixed_reads">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	153 <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"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	154 <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"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	155 <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" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	156 </when>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	157 </conditional>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	158 <param name="rna_strandness" type="select" label="Specify strand information"
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	159 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">
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	160 <option value="" selected="true">Unstranded</option>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	161 <option value="--fr">Forward (FR)</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	162 <option value="--rf">Reverse (RF)</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	163 </param>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	164 <conditional name="guide">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	165 <param name="use_guide" argument="-G" type="select" label="Use a reference file to guide assembly?" help="Use the reference annotation file (in GTF or GFF3 format) to guide the assembly process. The output will include expressed reference transcripts as well as any novel transcripts that are assembled. This option is required by option -e (Use Reference transcripts only), see below.">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	166 <option value="yes">Use reference GTF/GFF3</option>
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	167 <option value="no" selected="true" >Do not use reference GTF/GFF3</option>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	168 </param>
62d212192002 Imported from capsule None iuc parents: diff changeset	169 <when value="no" />
62d212192002 Imported from capsule None iuc parents: diff changeset	170 <when value="yes">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	171 <conditional name="guide_source">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	172 <param name="guide_gff_select" type="select" label="Reference file">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	173 <option value="cached" selected="true">Use a built-in file</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	174 <option value="history">Use a file from history</option>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	175 </param>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	176 <when value="cached">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	177 <param name="ref_builtin" type="select" label="Use a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	178 <options from_data_table="gene_sets">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	179 <filter type="sort_by" column="2" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	180 <validator type="no_options" message="No GTF file is available." />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	181 </options>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	182 </param>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	183 </when>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	184 <when value="history">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	185 <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	186 </when>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	187 </conditional>
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	188 <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Use Reference transcripts only?" help="Limit the processing of read alignments to only estimate and output the assembled transcripts matching the reference transcripts given with the -G option. With this option, read bundles with no reference transcripts (novel transcripts) will be entirely skipped, which may provide a considerable speed boost when the given set of reference transcripts is limited to a set of target genes, for example. Default: No"/>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	189 <conditional name="special_outputs">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	190 <param name="special_outputs_select" type="select" label="Output files for differential expression?" help="Select to output additional files that can be used with Ballgown or DESeq2/edgeR. See Help section below for more information">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	191 <option value="ballgown">Ballgown</option>
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	192 <option value="deseq2">DESeq2/edgeR/limma-voom</option>
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	193 <option value="no" selected="true">No additional output</option>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	194 </param>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	195 <when value="ballgown" />
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	196 <when value="deseq2">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	197 <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75" />
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	198 <param name="clustering" argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" checked="false" label="Cluster overlapping genes" help="Choose whether to cluster genes with different gene IDs that overlap. Transcripts containing the geneID prefix will be ignored. Default: No" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	199 <param argument="--string" type="text" label="Prefix used for transcripts" help="If a different prefix was used for geneIDs assigned by StringTie than the default, specify it here. Only letters and numbers will be retained in this field. Default: MSTRG" >
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	200 <sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	201 <valid initial="string.letters,string.digits"></valid>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	202 </sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	203 </param>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	204 <param argument="--key" type="text" label="Prefix for clustering" help="If clustering, what prefix to use for geneIDs assigned by this script. Only letters and numbers will be retained in this field. Default: prepG">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	205 <sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	206 <valid initial="string.letters,string.digits"></valid>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	207 </sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	208 </param>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	209 </when>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	210 <when value="no" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	211 </conditional>
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	212 <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."/>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	213 </when>
62d212192002 Imported from capsule None iuc parents: diff changeset	214 </conditional>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	215 <section name="adv" title="Advanced Options">
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	216 <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"/>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	217 <param name="omit_sequences" argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences. This parameter can be a single reference sequence name (e.g. chrM) or a comma-delimited list of sequence names (e.g. chrM,chrX,chrY). This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases, even though they may be of no interest for a particular RNA-Seq analysis. The reference sequence names are case sensitive, they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place." />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	218 <param name="name_prefix" argument="-l" type="text" label="Name prefix for output transcripts" help="This prefix will be added to the name of the transcripts that are output. Only letters and numbers will be retained in this field. Default: STRG">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	219 <sanitizer>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	220 <valid initial="string.letters,string.digits"></valid>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	221 </sanitizer>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	222 </param>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	223 <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.15" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.15"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	224 <param name="min_tlen" argument="-m" type="integer" min="0" value="200" label="Minimum assembled transcript length" help="Sets the minimum length allowed for the predicted transcripts. Default: 200"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	225 <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	226 <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	227 <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	228 <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	229 <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"/>
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	230 <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" />
eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	231 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/>
19 333a6e13b622 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938" iuc parents: 18 diff changeset	232 <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)."/>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	233 </section>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	234 </inputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	235 <outputs>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	236 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	237 <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates">
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	238 <filter>adv['abundance_estimation']</filter>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	239 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	240 <data name="coverage" format="gtf" label="${tool.name} on ${on_string}: Coverage">
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	241 <filter>guide['use_guide'] == 'yes' and guide['coverage_file'] is True </filter>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	242 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	243 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	244 label="${tool.name} on ${on_string}: exon-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	245 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	246 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	247 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	248 label="${tool.name} on ${on_string}: intron-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	249 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	250 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	251 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	252 label="${tool.name} on ${on_string}: transcript-level expression measurements">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	253 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	254 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	255 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	256 label="${tool.name} on ${on_string}: exon to transcript mapping">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	257 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	258 </data>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	259 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	260 label="${tool.name} on ${on_string}: intron to transcript mapping">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	261 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	262 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	263 <data name="gene_counts" format="tabular" from_work_dir="special_de_output/sample1/gene_counts.tsv" label="${tool.name} on ${on_string}: Gene counts">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	264 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	265 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	266 <data name="transcript_counts" format="tabular" from_work_dir="special_de_output/sample1/transcript_counts.tsv" label="${tool.name} on ${on_string}: Transcript counts">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	267 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	268 </data>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	269 <data name="legend" format="tabular" from_work_dir="special_de_output/sample1/legend.tsv" label="${tool.name} on ${on_string}: legend">
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	270 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	271 </data>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	272 </outputs>
62d212192002 Imported from capsule None iuc parents: diff changeset	273 <tests>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	274 <!--Ensure default GTF output works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	275 <test expect_num_outputs="1">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	276 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	277 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	278 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	279 </conditional>
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	280 <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	281 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	282 <!--Ensure fraction option works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	283 <test expect_num_outputs="1">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	284 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	285 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	286 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	287 </conditional>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	288 <param name="fraction" value="0.17" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	289 <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	290 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	291 <!--Ensure guide option works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	292 <test expect_num_outputs="1">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	293 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	294 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	295 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	296 </conditional>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	297 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	298 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	299 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	300 <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	301 </test>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	302 <!--Ensure guide with fraction works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	303 <test expect_num_outputs="1">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	304 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	305 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	306 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	307 </conditional>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	308 <param name="use_guide" value="yes" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	309 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	310 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	311 <param name="fraction" value="0.17" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	312 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	313 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	314 <!--Ensure coverage and output for Ballgown works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	315 <test expect_num_outputs="7">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	316 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	317 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	318 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	319 </conditional>
1 9f80c71f1779 Uploaded updated tool wrapper for stringtie 1.0.1 iuc parents: 0 diff changeset	320 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	321 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	322 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	323 <param name="special_outputs_select" value="ballgown" />
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	324 <param name="coverage_file" value="true" />
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	325 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	326 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	327 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	328 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	329 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	330 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/>
cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	331 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	332 </test>
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	333 <!--Ensure output for edgeR works -->
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	334 <test expect_num_outputs="5">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	335 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	336 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	337 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	338 </conditional>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	339 <param name="use_guide" value="yes" />
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	340 <param name="special_outputs_select" value="deseq2" />
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	341 <param name="input_estimation" value="true" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	342 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	343 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	344 <param name="coverage_file" value="true" />
eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	345 <param name="clustering" value="true" />
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	346 <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	347 <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" />
a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	348 <output name="legend" file="legend.tsv" ftype="tabular" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	349 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/>
cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	350 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	351 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	352 <!--Ensure gene abundances output works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	353 <test expect_num_outputs="2">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	354 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	355 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	356 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	357 </conditional>
10 c84d44519b2e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103 iuc parents: 7 diff changeset	358 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	359 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	360 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	361 <param name="fraction" value="0.17" />
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	362 <param name="abundance_estimation" value="true" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	363 <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/>
16 eba36e001f45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7dbb0fbe5446140f40fed36e45f42ec8d34bbc78 iuc parents: 15 diff changeset	364 <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	365 </test>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	366 <!--Ensure another fraction value works -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	367 <test expect_num_outputs="1">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	368 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	369 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	370 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	371 </conditional>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	372 <param name="use_guide" value="yes" />
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	373 <param name="guide_gff_select" value="history" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	374 <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	375 <param name="fraction" value="0.15" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	376 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	377 </test>
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	378 <!--Ensure built-in GTFs work -->
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	379 <test expect_num_outputs="1">
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	380 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	381 <param name="input_mode" value="short_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	382 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	383 </conditional>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	384 <param name="use_guide" value="yes" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	385 <param name="guide_gff_select" value="cached" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	386 <param name="fraction" value="0.15" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	387 <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/>
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	388 </test>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	389 <!-- Test long reads input -->
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	390 <test expect_num_outputs="1">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	391 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	392 <param name="input_mode" value="long_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	393 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	394 </conditional>
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	395 <param name="use_guide" value="yes" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	396 <param name="guide_gff_select" value="cached" />
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	397 <param name="fraction" value="0.15" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	398 <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	399 </test>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	400 <!-- Test error splice option -->
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	401 <test expect_num_outputs="1">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	402 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	403 <param name="input_mode" value="long_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	404 <param name="input_bam" ftype="bam" value="long_reads.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	405 <param name="error_splice" value="30" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	406 </conditional>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	407 <param name="use_guide" value="yes" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	408 <param name="guide_gff_select" value="cached" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	409 <param name="fraction" value="0.15" />
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	410 <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/>
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	411 </test>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	412 <!-- Test mixed reads input -->
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	413 <test expect_num_outputs="1">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	414 <conditional name="input_options">
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	415 <param name="input_mode" value="mixed_reads"/>
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	416 <param name="input_bam_short" ftype="bam" value="short_reads.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	417 <param name="input_bam_long" ftype="bam" value="long_reads.bam" />
258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	418 </conditional>
20 cef79931dda5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 7f649c10c5d874f466122af0d24803a4c6affabb iuc parents: 19 diff changeset	419 <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" compare="re_match" sort="true"/>
5 f504b3b7e49d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 65c9ce2fdc2b4ce892df8e456f18b859a85c410a iuc parents: 4 diff changeset	420 </test>
0 62d212192002 Imported from capsule None iuc parents: diff changeset	421 </tests>
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	422 <help><![CDATA[
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	423
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	424 .. class:: infomark
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	425
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	426 What it does
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	427
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	428 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.).
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	429
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	430 -----
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	431
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	432 Inputs
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	433
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	434 StringTie takes as input a BAM (or SAM) file of paired-end RNA-seq reads, which must be sorted by genomic location (coordinate position). This file contains spliced read alignments and can be produced directly by programs such as HISAT2_. We recommend using HISAT2 as it is a fast and accurate alignment program. Every spliced read alignment (i.e. an alignment across at least one junction) in the input BAM file must contain the tag XS to indicate the genomic strand that produced the RNA from which the read was sequenced. Alignments produced by HISAT2 (when run with --dta option) already include this tag, but if you use a different read mapper you should check that this XS tag is included for spliced alignments.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	435
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	436 NOTE: be sure to run HISAT2 with the --dta option for alignment (under Spliced alignment options), or your results will suffer.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	437
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	438 Also note that if your reads are from a stranded library, you need to choose the appropriate setting under Specify strand information above. As, if Forward (FR) is selected, StringTie will assume the reads are from a --fr library, while if Reverse (RF) is selected, StringTie will assume the reads are from a --rf library, otherwise it is assumed that the reads are from an unstranded library (The widely-used, although now deprecated, TopHat had a similar --library-type option, where fr-firststrand corresponded to RF; fr-secondstrand corresponded to FR). If you don't know whether your reads are from are a stranded library or not, you could use the tool RSeQC Infer Experiment to try to determine.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	439
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	440 As an option, a reference annotation file in `GTF/GFF3`_ format can be provided to StringTie. In this case, StringTie will prefer to use these "known" genes from the annotation file, and for the ones that are expressed it will compute coverage, TPM and FPKM values. It will also produce additional transcripts to account for RNA-seq data that aren't covered by (or explained by) the annotation. Note that if option -e is not used the reference transcripts need to be fully covered by reads in order to be included in StringTie's output. In that case, other transcripts assembled from the data by StringTie and not present in the reference file will be printed as well.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	441
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	442 NOTE: we highly recommend that you provide annotation if you are analyzing a genome that is well-annotated, such as human, mouse, or other model organisms.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	443
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	444 -----
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	445
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	446 Outputs
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	447
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	448 StringTie's primary output is
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	449
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	450 * a GTF file containing the Assembled transcripts
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	451
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	452 Optionally, it can output
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	453
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	454 * a TSV (tab-delimited) file of Gene abundances
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	455
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	456 If a reference GTF/GFF3 file is used as a guide, StringTie can also output:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	457
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	458 * a GTF file containing all fully-covered reference transcripts in the provided reference file that are covered end-to-end by reads
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	459 * Files (tables) for Ballgown and/or DESeq2/edgeR/limma-voom, which can use them to estimate differential expression
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	460
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	461
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	462 StringTie's primary GTF output
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	463
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	464 The primary output of StringTie is a Gene Transfer Format (GTF) file that contains details of the transcripts that StringTie assembles from RNA-Seq data. GTF is an extension of GFF (Gene Finding Format, also called General Feature Format), and is very similar to GFF2 and GFF3. The field definitions for the 9 columns of GTF output can be found at the `Ensembl site here`_. The following is an example of a transcript assembled by StringTie as shown in a GTF file:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	465
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	466 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	467 seqname source feature start end score strand frame attributes
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	468 ----------- ---------- ----------- --------- ------- --------- ---------- --------- -------------------------------------------------------------------------------------------
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	469 chrX StringTie transcript 281394 303355 1000 \+ . gene_id "ERR188044.1"; transcript_id "ERR188044.1.1"; reference_id "NM_018390"; ref_gene_id
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	470 "NM_018390"; ref_gene_name "PLCXD1"; cov "101.256691"; FPKM "530.078918"; TPM "705.667908";
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	471 chrX StringTie exon 281394 281684 1000 \+ . gene_id "ERR188044.1"; transcript_id "ERR188044.1.1"; exon_number "1"; reference_id
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	472 "NM_018390"; ref_gene_id "NM_018390"; ref_gene_name "PLCXD1"; cov "116.270836";
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	473 =========== ========== =========== ========= ======= ========= ========== ========= ===========================================================================================
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	474
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	475
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	476 * seqname: Denotes the chromosome, contig, or scaffold for this transcript. Here the assembled transcript is on chromosome X.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	477
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	478 * source: The source of the GTF file. Since this example was produced by StringTie, this column simply shows 'StringTie'.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	479
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	480 * feature: Feature type (e.g., exon, transcript, mRNA, 5'UTR).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	481
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	482 * start: Start position of the feature (exon, transcript, etc), using a 1-based index.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	483
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	484 * end: End position of the feature, using a 1-based index.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	485
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	486 * score: A confidence score for the assembled transcript. Currently this field is not used, and StringTie reports a constant value of 1000 if the transcript has a connection to a read alignment bundle.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	487
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	488 * strand: If the transcript resides on the forward strand, '+'. If the transcript resides on the reverse strand, '-'.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	489
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	490 * frame: Frame or phase of CDS features. StringTie does not use this field and simply records a ".".
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	491
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	492 * attributes: A semicolon-separated list of tag-value pairs, providing additional information about each feature. Depending on whether an instance is a transcript or an exon and on whether the transcript matches the reference annotation file provided by the user, the content of the attributes field will differ. The following list describes the possible attributes shown in this column:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	493
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	494 * gene_id: A unique identifier for a single gene and its child transcript and exons based on the alignments' file name.
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	495
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	496 * transcript_id: A unique identifier for a single transcript and its child exons based on the alignments' file name.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	497
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	498 * exon_number: A unique identifier for a single exon, starting from 1, within a given transcript.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	499
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	500 * reference_id: The transcript_id in the reference annotation (optional) that the instance matched.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	501
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	502 * ref_gene_id: The gene_id in the reference annotation (optional) that the instance matched.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	503
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	504 * ref_gene_name: The gene_name in the reference annotation (optional) that the instance matched.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	505
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	506 * cov: The average per-base coverage for the transcript or exon.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	507
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	508 * FPKM: Fragments per kilobase of transcript per million read pairs. This is the number of pairs of reads aligning to this feature, normalized by the total number of fragments sequenced (in millions) and the length of the transcript (in kilobases).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	509
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	510 * TPM: Transcripts per million. This is the number of transcripts from this particular gene normalized first by gene length, and then by sequencing depth (in millions) in the sample. A detailed explanation and a comparison of TPM and FPKM can be found here_, and TPM was defined `by B. Li and C. Dewey here`_.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	511
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	512
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	513 Gene abundances in tab-delimited format
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	514
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	515 If StringTie is run with the -A option, it returns a file containing gene abundances. The tab-delimited gene abundances output file has nine fields; below is an example of a gene abundance file produced by StringTie using reference annotation:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	516
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	517 =========== ============= ============= ========== ========= ======= ============ ======== ========
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	518 Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	519 ----------- ------------- ------------- ---------- --------- ------- ------------ -------- --------
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	520 NM_000451 SHOX chrX \+ 624344 646823 0.000000 0.000000 0.000000
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	521 NM_006883 SHOX chrX \+ 624344 659411 0.000000 0.000000 0.000000
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	522 =========== ============= ============= ========== ========= ======= ============ ======== ========
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	523
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	524 * Gene ID: The gene identifier comes from the reference annotation provided with the -G option. If no reference is provided this field is replaced with the name prefix for output transcripts (-l).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	525 * Gene Name: This field contains the gene name in the reference annotation provided with the -G option. If no reference is provided this field is populated with '-'.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	526 * Reference: Name of the reference sequence that was used in the alignment of the reads. Equivalent to the 3rd column in the .SAM alignment.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	527 * Strand: '+' denotes that the gene is on the forward strand, '-' for the reverse strand.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	528 * Start: Start position of the gene (1-based index).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	529 * End: End position of the gene (1-based index).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	530 * Coverage: Per-base coverage of the gene.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	531 * FPKM: normalized expression level in FPKM units (see previous section).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	532 * TPM: normalized expression level in RPM units (see previous section).
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	533
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	534 Fully covered transcripts matching the reference annotation transcripts (in GTF format)
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	535
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	536 If StringTie is run with the use reference guide option (-G), it will also return a file with all the transcripts in the reference annotation that are fully covered, end to end, by reads. The output format is a GTF file as described above. Each line of the GTF is corresponds to a gene or transcript in the reference annotation.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	537
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	538 Ballgown Input Table Files
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	539
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	540 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.
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	541
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	542
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	543 DESeq2/edgeR/limma-voom Input Table Files
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	544
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	545 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.
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	546
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	547 -----
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	548
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	549 More Information
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	550
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	551 Evaluating transcript assemblies:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	552 A simple way of getting more information about the transcripts assembled by StringTie (summary of gene and transcript counts, novel vs. known etc.), or even performing basic tracking of assembled isoforms across multiple RNA-Seq experiments, is to use the gffcompare program. Basic usage information for this program can be found on the `GFF utilities page`_.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	553
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	554 Differential expression analysis:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	555
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	556 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`_.
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	557
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	558 Our recommended workflow includes the following steps:
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	559
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	560 1. For each RNA-Seq sample, map the reads to the genome with HISAT2 using the --dta option. It is highly recommended to use the reference annotation information when mapping the reads, which can be either embedded in the genome index (built with the --ss and --exon options, see HISAT2 manual), or provided separately at run time (using the --known-splicesite-infile option of HISAT2). The SAM output of each HISAT2 run must be sorted and converted to BAM using samtools as explained above.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	561
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	562 2. For each RNA-Seq sample, use this StringTie tool to assemble the read alignments obtained in the previous step; it is recommended to run StringTie with the -G option if the reference annotation is available.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	563
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	564 3. Run the separate StringTie merge tool in order to generate a non-redundant set of transcripts observed in all the RNA-Seq samples assembled previously. ``StringTie merge`` takes as input a list of all the assembled transcripts files (in GTF format) previously obtained for each sample, as well as a reference annotation file (-G option) if available.
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	565
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	566 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.)
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	567
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	568 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.
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	569
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	570 An alternate, faster differential expression analysis workflow can be pursued if there is no interest in novel isoforms (i.e. assembled transcripts present in the samples but missing from the reference annotation), or if only a well known set of transcripts of interest are targeted by the analysis. This simplified protocol has only 3 steps (depicted in the `StringTie manual here`_) as it bypasses the individual assembly of each RNA-Seq sample and the "transcript merge" step. This simplified workflow attempts to directly estimate and analyze the expression of a known set of transcripts as given in the reference annotation file.
0 62d212192002 Imported from capsule None iuc parents: diff changeset	571
2 520e0988ec1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b03fd81ed11744f119608d4884c24fa182eb605a iuc parents: 1 diff changeset	572 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	573 .. _Ballgown: https://www.biorxiv.org/content/early/2014/09/05/003665
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	574 .. _Cuffdiff: http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	575 .. _DESeq2: https://bioconductor.org/packages/release/bioc/html/DESeq2.html
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	576 .. _edgeR: https://bioconductor.org/packages/release/bioc/html/edgeR.html
15 dd4df992d93d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a834a41c94d184df80e45ffa2339723826a075b1 iuc parents: 14 diff changeset	577 .. _limma: https://bioconductor.org/packages/release/bioc/html/limma.html
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	578 .. _Bioconductor: https://www.bioconductor.org/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	579 .. _SAM: http://samtools.github.io/hts-specs/SAMv1.pdf
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	580 .. _HISAT2: http://ccb.jhu.edu/software/hisat2
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	581 .. _`GTF/GFF3`: http://ccb.jhu.edu/software/stringtie/gff.shtml
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	582 .. _`this link`: https://github.com/alyssafrazee/ballgown#ballgown-readable-expression-output
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	583 .. _`Ensembl site here`: http://useast.ensembl.org/info/website/upload/gff.html
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	584 .. _here: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/
76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	585 .. _`by B. Li and C. Dewey here`: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	586 .. _`GFF utilities page`: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	587 .. _`protocol paper`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/
18 258d696dbd7e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" iuc parents: 17 diff changeset	588 .. _`StringTie manual here`: http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual
12 76d290331481 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 iuc parents: 11 diff changeset	589
11 6e45b443ef1f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf iuc parents: 10 diff changeset	590 ]]></help>
6 d0bb240d7525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 iuc parents: 5 diff changeset	591 <expand macro="citations" />
13 a305d75e13f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit e811a7887db870f4f94f620f52bce656c8d5ba23 iuc parents: 12 diff changeset	592 </tool>

Mercurial > repos > iuc > stringtie

annotate stringtie.xml @ 20:cef79931dda5 draft