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annotate stringtie.xml @ 15:457d00d0005d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
author iuc
date Tue, 04 Apr 2017 12:58:13 -0400
parents f70601406e0e
children bc451c12cd18
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15
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
iuc
parents: 12
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1 <tool id="stringtie" name="StringTie" version="1.3.3">
8
6884408acc44 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 92a9d47a3807a276aa98a38d38e6f0f8caa12389
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2 <description>transcript assembly and quantification</description>
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parents: 11
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3 <macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
iuc
parents: 11
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4 <import>macros.xml</import>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
iuc
parents: 11
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5 </macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
iuc
parents: 11
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6 <expand macro="requirements" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
iuc
parents: 11
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7 <expand macro="stdio" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
iuc
parents: 11
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8 <expand macro="version_command" />
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
iuc
parents: 11
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9 <command>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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10 <![CDATA[
15
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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11 mkdir -p ./special_de_output/sample1/ &&
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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parents: 12
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12 #if str($guide.use_guide) == 'yes':
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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13 ln -s '$guide.guide_gff' ./special_de_output/sample1/guide.gtf &&
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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14 #end if
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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15
12
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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16 #if $input_bam.metadata.ftype == 'sam':
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457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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17 samtools sort -@ \${GALAXY_SLOTS:-1} '$input_bam' | stringtie
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f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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18 #else
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457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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19 stringtie '$input_bam'
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20 #end if
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457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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21
12
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22 -o "$output_gtf"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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23 -p "\${GALAXY_SLOTS:-1}"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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24 #if str($guide.use_guide) == 'yes':
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457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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25 -C '$coverage'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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26 -G '$guide.guide_gff'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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27 $guide.input_estimation
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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28 #if $guide.special_outputs != 'no':
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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29 -b ./special_de_output/sample1/
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30 #end if
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f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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31 #end if
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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32 #if str($option_set.options) == 'advanced':
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33 -l '$option_set.name_prefix'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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34 -f '$option_set.fraction'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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35 -m '$option_set.min_tlen'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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36 -a '$option_set.min_anchor_len'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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37 -j '$option_set.min_anchor_cov'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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38 -c '$option_set.min_bundle_cov'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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39 -g '$option_set.bdist'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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40 -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
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41 #if $option_set.abundance_estimation:
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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42 -A "$gene_abundance_estimation"
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43 #end if
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44 #if str($option_set.omit_sequences).strip() != "":
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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45 -x "$option_set.omit_sequences"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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46 #end if
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47 #end if
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48
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49 #if str($guide.use_guide) == 'yes':
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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50 #if $guide.special_outputs.special_outputs_select == 'deseq2':
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51 &&
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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52 prepDE.py
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53 -i ./special_de_output/
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54 -g gene_cout_matrix.tsv
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55 -t transcripts_count_matrix.tsv
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56 -l $guide.special_outputs.read_length
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57 #if str($option_set.options) == 'advanced':
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58 -s '$option_set.name_prefix'
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59 #end if
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60 #if $guide.special_outputs.clustering:
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61 -c
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62 --legend ./legend.tsv
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63
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64 &&
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65 sed -i.bak 's/,/\t/g' ./legend.tsv
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66
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67 #end if
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68 &&
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69 sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv
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70 &&
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71 sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv
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72 #end if
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73 #end if
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74
12
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75 ]]>
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76 </command>
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77 <inputs>
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78 <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />
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79 <conditional name="guide">
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80 <param label="Use GFF file to guide assembly" name="use_guide" type="select">
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81 <option value="yes">Use GFF/GTF</option>
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82 <option selected="True" value="no">Do not use GFF/GTF</option>
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83 </param>
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84 <when value="no" />
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85 <when value="yes">
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86 <param argument="-G" format="gtf,gff3" name="guide_gff" type="data"
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87 help="" label="Reference annotation to use for guiding the assembly process" />
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88 <param argument="-e" name="input_estimation" truevalue="-e" type="boolean" falsevalue=""
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89 help="" label="Perform abundance estimation only of input transcripts" />
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90 <conditional name="special_outputs">
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91 <param label="Output additional files for use in..." name="special_outputs_select" type="select">
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92 <option value="ballgown">Ballgown</option>
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93 <option selected="True" value="deseq2">DESeq2/EdgeR</option>
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94 <option value="no">No addional output</option>
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95 </param>
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96 <when value="ballgown" />
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97 <when value="deseq2">
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98 <param label="Average read length" name="read_length" type="integer" value="75" help="" />
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99 <param label="Whether to cluster genes that overlap with different gene IDs"
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100 name="clustering"
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101 truevalue="--cluster"
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102 type="boolean" help="ignoring ones with geneID pattern" falsevalue="" />
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103 </when>
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104 </conditional>
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105 </when>
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106 </conditional>
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107 <conditional name="option_set">
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108 <param help="" label="Options" name="options" type="select">
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109 <option selected="True" value="default">Use defaults</option>
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110 <option value="advanced">Specify advanced options</option>
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111 </param>
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112 <when value="default" />
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113 <when value="advanced">
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114 <param argument="-t" falsevalue="" name="disable_trimming" truevalue="-t" type="boolean"
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115 label="Disable trimming of predicted transcripts based on coverage" />
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116 <param argument="-S" falsevalue=""
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117 label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
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118 <param argument="-l" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
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119 <param argument="-f" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
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120 <param argument="-m" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
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121 <param argument="-a" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
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122 <param argument="-j" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
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123 <param argument="-c" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
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124 <param argument="-g" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
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125 <param argument="-M" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
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126 <param argument="-x" name="omit_sequences" type="text" value=""
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127 help="e.g. chrM,chrX" label="Do not assemble any transcripts on these reference sequence(s)" />
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128 <param argument="-A" falsevalue="" name="abundance_estimation" truevalue="-A" type="boolean"
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129 label="Additional gene abundance estimation output file" />
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130 <param argument="-u" falsevalue="" truevalue="-u" type="boolean"
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131 label="Disable multi-mapping correction" name="multi_mapping" />
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132 </when>
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133 </conditional>
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134 </inputs>
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135 <outputs>
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136 <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
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137 <data format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates" name="gene_abundance_estimation">
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138 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
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139 </data>
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140 <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
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141 <filter>guide['use_guide'] == 'yes'</filter>
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142 </data>
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143 <data format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
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144 label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
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145 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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146 </data>
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147 <data format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
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148 label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
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149 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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150 </data>
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151 <data format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
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152 label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
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153 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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154 </data>
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155 <data format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
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156 label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
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157 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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158 </data>
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159 <data format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
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160 label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
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161 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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162 </data>
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163
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164 <data format="tabular" from_work_dir="gene_cout_matrix.tsv"
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165 label="${tool.name} on ${on_string}: Gene counts" name="gene_counts">
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166 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
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167 </data>
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168 <data format="tabular" from_work_dir="transcripts_count_matrix.tsv"
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169 label="${tool.name} on ${on_string}: Transcript counts" name="transcript_counts">
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170 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
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171 </data>
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172 <data format="tabular" from_work_dir="legend.tsv"
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173 label="${tool.name} on ${on_string}: legend" name="legend">
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174 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2' and guide['special_outputs']['clustering'] is True</filter>
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175 </data>
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176 </outputs>
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177 <tests>
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178 <test>
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179 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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180 <param name="use_guide" value="no" />
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181 <param name="options" value="default" />
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182 <output file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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183 </test>
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184 <test>
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185 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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186 <param name="use_guide" value="no" />
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187 <param name="options" value="advanced" />
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188 <param name="fraction" value="0.17" />
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189 <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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190 </test>
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191 <test>
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192 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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193 <param name="use_guide" value="yes" />
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194 <param name="special_outputs_select" value="no" />
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195 <param name="guide_gff" value="stringtie_in.gtf" />
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196 <param name="options" value="default" />
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197 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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198 </test>
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199 <test>
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200 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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201 <param name="use_guide" value="yes" />
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202 <param name="special_outputs_select" value="no" />
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203 <param name="guide_gff" value="stringtie_in.gtf" />
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204 <param name="options" value="advanced" />
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205 <param name="fraction" value="0.17" />
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206 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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207 </test>
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208 <test>
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209 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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210 <param name="use_guide" value="yes" />
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211 <param name="special_outputs_select" value="ballgown" />
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212 <param name="guide_gff" value="stringtie_in.gtf" />
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213 <param name="options" value="default" />
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214 <output file="./ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
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215 <output file="./ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
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216 <output file="./ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
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217 <output file="./ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
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218 <output file="./ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
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219 <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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220 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
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221 </test>
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222 <test>
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223 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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224 <param name="use_guide" value="yes" />
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225 <param name="special_outputs_select" value="deseq2" />
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226 <param name="input_estimation" value="True" />
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227 <param name="guide_gff" value="stringtie_in.gtf" />
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228 <param name="options" value="default" />
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229 <param name="clustering" value="True" />
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230 <output file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" name="gene_counts" />
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231 <output file="./deseq2/transcript_counts.tsv" ftype="tabular" name="transcript_counts" />
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232 <output file="./deseq2/legend.tsv" ftype="tabular" name="legend" />
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233 <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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234 <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
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235 </test>
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236 <test>
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237 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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238 <param name="use_guide" value="yes" />
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239 <param name="guide_gff" value="stringtie_in.gtf" />
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240 <param name="options" value="advanced" />
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241 <param name="fraction" value="0.17" />
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242 <param name="abundance_estimation" value="True" />
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243 <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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244 <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />
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245 </test>
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246 <test>
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247 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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248 <param name="use_guide" value="yes" />
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249 <param name="special_outputs_select" value="no" />
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250 <param name="guide_gff" value="stringtie_in.gtf" />
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251 <param name="options" value="advanced" />
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252 <param name="fraction" value="0.15" />
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253 <param name="c" value="test_chromosome" />
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254 <output file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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255 </test>
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256 </tests>
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257 <help>
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258 <![CDATA[
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259
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260 **What it does?**
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261
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262 StringTie_ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional *de novo* assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.To identify differentially expressed genes between experiments, StringTie's output can be processed either by the Cuffdiff or Ballgown programs.
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263
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264 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
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265
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266 ------
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267
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268 StringTie has the following options::
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269
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270 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
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271 -l name prefix for output transcripts (default: STRG)
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272 -f minimum isoform fraction (default: 0.1)
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273 -m minimum assembled transcript length (default: 200)
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274 -o output path/file name for the assembled transcripts GTF (default: stdout)
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275 -a minimum anchor length for junctions (default: 10)
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276 -j minimum junction coverage (default: 1)
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277 -t disable trimming of predicted transcripts based on coverage
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278 (default: coverage trimming is enabled)
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279 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
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280 -v verbose (log bundle processing details)
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281 -g gap between read mappings triggering a new bundle (default: 50)
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282 -C output file with reference transcripts that are covered by reads
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283 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
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284 -p number of threads (CPUs) to use (default: 1)
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285 -A gene abundance estimation output file
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286 -B enable output of Ballgown table files which will be created in the
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287 same directory as the output GTF (requires -G, -o recommended)
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288 -b enable output of Ballgown table files but these files will be
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289 created under the directory path given as <dir_path>
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290 -e only estimates the abundance of given reference transcripts (requires -G)
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291 -x do not assemble any transcripts on these reference sequence(s)
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292 -u no multi-mapping correction default: false)
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293
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294 ]]>
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295 </help>
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296 <expand macro="citations" />
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297 </tool>