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annotate stringtie.xml @ 16:bc451c12cd18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf
author iuc
date Thu, 01 Jun 2017 12:15:51 -0400
parents 457d00d0005d
children d2d010512422
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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">
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2 <description>transcript assembly and quantification</description>
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3 <macros>
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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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
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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
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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
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8 <expand macro="version_command" />
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bc451c12cd18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit d46e597732cda927a633e133c14dd4ece39f5edf
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9 <command><![CDATA[
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10 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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11 #if str($guide.use_guide) == 'yes':
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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12 ln -s '$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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13 #end if
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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14
12
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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15 #if $input_bam.metadata.ftype == 'sam':
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457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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16 samtools sort -@ \${GALAXY_SLOTS:-1} '$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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17 #else
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18 stringtie '$input_bam'
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19 #end if
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20
12
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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21 -o "$output_gtf"
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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22 -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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23 #if str($guide.use_guide) == 'yes':
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24 -C '$coverage'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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25 -G '$guide.guide_gff'
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26 $guide.input_estimation
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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27 #if $guide.special_outputs != 'no':
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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28 -b ./special_de_output/sample1/
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29 #end if
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30 #end if
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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31 #if str($option_set.options) == 'advanced':
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32 -l '$option_set.name_prefix'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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33 -f '$option_set.fraction'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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34 -m '$option_set.min_tlen'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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35 -a '$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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36 -j '$option_set.min_anchor_cov'
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37 -c '$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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38 -g '$option_set.bdist'
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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39 -M '$option_set.bundle_fraction' $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping
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40 #if $option_set.abundance_estimation:
f70601406e0e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 15099b938e3ef54150ebf6b67969c27928c763c0
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41 -A "$gene_abundance_estimation"
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42 #end if
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43 #if str($option_set.omit_sequences).strip() != "":
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44 -x '$option_set.omit_sequences'
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45 #end if
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
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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48 #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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49 #if $guide.special_outputs.special_outputs_select == 'deseq2':
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50 &&
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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51 prepDE.py
457d00d0005d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit b78c073ab258852730fc9af1cd4862d571459103
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52 -i ./special_de_output/
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53 -g gene_cout_matrix.tsv
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54 -t transcripts_count_matrix.tsv
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55 -l $guide.special_outputs.read_length
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56 #if str($option_set.options) == 'advanced':
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57 -s '$option_set.name_prefix'
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58 #end if
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59 #if $guide.special_outputs.clustering:
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60 -c
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61 --legend ./legend.tsv
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62
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63 &&
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64 sed -i.bak 's/,/\t/g' ./legend.tsv
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65
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66 #end if
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67 &&
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68 sed -i.bak 's/,/\t/g' transcripts_count_matrix.tsv
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69 &&
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70 sed -i.bak 's/,/\t/g' gene_cout_matrix.tsv
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71 #end if
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72 #end if
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73 ]]></command>
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74 <inputs>
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75 <param name="input_bam" type="data" format="sam,bam" label="Mapped reads to assemble transcripts from" />
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76 <conditional name="guide">
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77 <param name="use_guide" type="select" label="Use GFF file to guide assembly">
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78 <option value="yes">Use GFF/GTF</option>
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79 <option selected="True" value="no">Do not use GFF/GTF</option>
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80 </param>
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81 <when value="no" />
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82 <when value="yes">
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83 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3"
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84 label="Reference annotation to use for guiding the assembly process" />
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85 <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue=""
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86 label="Perform abundance estimation only of input transcripts" />
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87 <conditional name="special_outputs">
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88 <param name="special_outputs_select" type="select" label="Output additional files for use in...">
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89 <option value="ballgown">Ballgown</option>
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90 <option selected="True" value="deseq2">DESeq2/EdgeR</option>
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91 <option value="no">No addional output</option>
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92 </param>
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93 <when value="ballgown" />
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94 <when value="deseq2">
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95 <param name="read_length" type="integer" value="75" label="Average read length" />
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96 <param name="clustering" type="boolean" truevalue="--cluster" falsevalue="" label="Whether to cluster genes that overlap with different gene IDs" help="ignoring ones with geneID pattern" />
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97 </when>
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98 <when value="no" />
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99 </conditional>
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100 </when>
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101 </conditional>
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102 <conditional name="option_set">
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103 <param name="options" type="select" label="Options">
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104 <option selected="True" value="default">Use defaults</option>
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105 <option value="advanced">Specify advanced options</option>
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106 </param>
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107 <when value="default" />
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108 <when value="advanced">
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109 <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue=""
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110 label="Disable trimming of predicted transcripts based on coverage" />
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111 <param name="sensitive" argument="-S" type="boolean" truevalue="-S" falsevalue=""
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112 label="Increase sensitivity" />
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113 <param name="name_prefix" argument="-l" type="text" value="STRG" label="Name prefix for output transcripts" />
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114 <param name="fraction" argument="-f" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
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115 <param name="min_tlen" argument="-m" type="integer" value="200" label="Minimum assembled transcript length" />
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116 <param name="min_anchor_len" argument="-a" type="integer" value="10" label="Minimum anchor length for junctions" />
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117 <param name="min_anchor_cov" argument="-j" type="integer" value="1" label="Minimum junction coverage" />
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118 <param name="min_bundle_cov" argument="-c" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
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119 <param name="bdist" argument="-g" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
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120 <param name="bundle_fraction" argument="-M" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
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121 <param name="omit_sequences" argument="-x" type="text" value=""
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122 label="Do not assemble any transcripts on these reference sequence(s)" help="e.g. chrM,chrX" />
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123 <param name="abundance_estimation" argument="-A" type="boolean" truevalue="-A" falsevalue=""
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124 label="Additional gene abundance estimation output file" />
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125 <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue=""
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126 label="Disable multi-mapping correction" />
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127 </when>
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128 </conditional>
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129 </inputs>
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130 <outputs>
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131 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" />
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132 <data name="gene_abundance_estimation" format="gtf" label="${tool.name} on ${on_string}: Gene abundance estimates">
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133 <filter>option_set['options'] == 'advanced' and option_set['abundance_estimation']</filter>
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134 </data>
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135 <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
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136 <filter>guide['use_guide'] == 'yes'</filter>
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137 </data>
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138 <data name="exon_expression" format="tabular" from_work_dir="special_de_output/sample1/e_data.ctab"
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139 label="${tool.name} on ${on_string}: exon-level expression measurements">
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140 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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141 </data>
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142 <data name="intron_expression" format="tabular" from_work_dir="special_de_output/sample1/i_data.ctab"
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143 label="${tool.name} on ${on_string}: intron-level expression measurements">
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144 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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145 </data>
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146 <data name="transcript_expression" format="tabular" from_work_dir="special_de_output/sample1/t_data.ctab"
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147 label="${tool.name} on ${on_string}: transcript-level expression measurements">
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148 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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149 </data>
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150 <data name="exon_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/e2t.ctab"
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151 label="${tool.name} on ${on_string}: exon to transcript mapping">
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152 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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153 </data>
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154 <data name="intron_transcript_mapping" format="tabular" from_work_dir="special_de_output/sample1/i2t.ctab"
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155 label="${tool.name} on ${on_string}: intron to transcript mapping">
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156 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'ballgown'</filter>
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157 </data>
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158 <data name="gene_counts" format="tabular" from_work_dir="gene_cout_matrix.tsv"
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159 label="${tool.name} on ${on_string}: Gene counts">
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160 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
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161 </data>
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162 <data name="transcript_counts" format="tabular" from_work_dir="transcripts_count_matrix.tsv"
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163 label="${tool.name} on ${on_string}: Transcript counts">
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164 <filter>guide['use_guide'] == 'yes' and guide['special_outputs']['special_outputs_select'] == 'deseq2'</filter>
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165 </data>
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166 <data name="legend" format="tabular" from_work_dir="legend.tsv"
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167 label="${tool.name} on ${on_string}: legend">
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168 <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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169 </data>
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170 </outputs>
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171 <tests>
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172 <test>
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173 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
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174 <param name="use_guide" value="no" />
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175 <param name="options" value="default" />
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176 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" lines_diff="2" />
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177 </test>
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178 <test>
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179 <param name="input_bam" ftype="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="advanced" />
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182 <param name="fraction" value="0.17" />
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183 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" />
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184 </test>
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185 <test>
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186 <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
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187 <param name="use_guide" value="yes" />
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188 <param name="special_outputs_select" value="no" />
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189 <param name="guide_gff" value="stringtie_in.gtf" />
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190 <param name="options" value="default" />
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191 <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />
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192 </test>
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193 <test>
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194 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
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195 <param name="use_guide" value="yes" />
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196 <param name="special_outputs_select" value="no" />
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197 <param name="guide_gff" value="stringtie_in.gtf" />
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198 <param name="options" value="advanced" />
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199 <param name="fraction" value="0.17" />
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200 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" />
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201 </test>
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202 <test>
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203 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
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204 <param name="use_guide" value="yes" />
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205 <param name="special_outputs_select" value="ballgown" />
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206 <param name="guide_gff" value="stringtie_in.gtf" />
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207 <param name="options" value="default" />
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208 <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" />
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209 <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" />
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210 <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" />
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211 <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" />
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212 <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" />
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213 <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" />
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214 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gff3" />
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215 </test>
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216 <test>
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217 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
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218 <param name="use_guide" value="yes" />
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219 <param name="special_outputs_select" value="deseq2" />
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220 <param name="input_estimation" value="True" />
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221 <param name="guide_gff" value="stringtie_in.gtf" />
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222 <param name="options" value="default" />
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223 <param name="clustering" value="True" />
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224 <output name="gene_counts" file="./deseq2/gene_counts.tsv" ftype="tabular" lines_diff="2" />
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225 <output name="transcript_counts" file="./deseq2/transcript_counts.tsv" ftype="tabular" />
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226 <output name="legend" file="./deseq2/legend.tsv" ftype="tabular" />
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227 <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" />
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228 <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gff3" />
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229 </test>
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230 <test>
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231 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
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232 <param name="use_guide" value="yes" />
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233 <param name="guide_gff" value="stringtie_in.gtf" />
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234 <param name="options" value="advanced" />
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235 <param name="fraction" value="0.17" />
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236 <param name="abundance_estimation" value="True" />
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237 <output name="output_gtf" file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" />
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238 <output name="gene_abundance_estimation" file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" />
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239 </test>
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240 <test>
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241 <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />
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242 <param name="use_guide" value="yes" />
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243 <param name="special_outputs_select" value="no" />
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244 <param name="guide_gff" value="stringtie_in.gtf" />
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245 <param name="options" value="advanced" />
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246 <param name="fraction" value="0.15" />
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247 <param name="c" value="test_chromosome" />
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248 <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2" />
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249 </test>
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250 </tests>
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251 <help><![CDATA[
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252 **What it does?**
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253
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254 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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255
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256 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
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257 ]]></help>
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258 <expand macro="citations" />
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259 </tool>