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1 <?xml version="1.0"?>
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2 <tool name="StringTie" id="stringtie" version="1.0.0">
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3 <description>RNA-Seq assembler</description>
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4 <requirements>
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5 <requirement type="package" version="0.97">stringtie</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 stringtie "$input_bam"
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10 -o "$output_gtf"
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11 -p "\${GALAXY_SLOTS:-1}"
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12 #if str($guide.use_guide) == 'yes':
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13 -G "$guide.guide_gff" $guide.input_estimation
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14 -C "$coverage"
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15 #end if
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16 #if str($option_set.options) == 'advanced':
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17 -f "$option_set.fraction"
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18 -m "$option_set.min_tlen"
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19 -a "$option_set.min_anchor_len"
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20 -j "$option_set.min_anchor_cov"
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21 -c "$option_set.min_bundle_cov"
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22 -s "$option_set.maxcov"
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23 -g "$option_set.bdist"
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24 -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
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25 #end if
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param name="input_bam" type="data" format="bam" label="BAM file to assemble" />
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30 <conditional name="guide">
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31 <param name="use_guide" type="select" label="Use GFF file to guide assembly">
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32 <option value="yes">Use GFF</option>
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33 <option value="no" selected="True">Do not use GFF</option>
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34 </param>
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35 <when value="no" />
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36 <when value="yes">
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37 <param name="guide_gff" type="data" format="gtf,gff3" label="Reference annotation to use for guiding the assembly process" />
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38 <param name="input_estimation" type="boolean" truevalue="-e" falsevalue="" label="Perform abundance estimation only of input transcripts" />
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39 </when>
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40 </conditional>
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41 <conditional name="option_set">
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42 <param name="options" type="select" label="Options">
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43 <option value="default" selected="True">Use defaults</option>
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44 <option value="advanced">Specify advanced options</option>
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45 </param>
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46 <when value="default" />
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47 <when value="advanced">
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48 <param name="disable_trimming" type="boolean" falsevalue="" truevalue="-t" label="Disable trimming of predicted transcripts based on coverage" />
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49 <param name="sensitive" type="boolean" truevalue="-S" falsevalue="" label="Increase sensitivity" />
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50 <param name="fraction" type="float" value="0.15" min="0.0" max="1.0" label="Minimum isoform fraction" />
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51 <param name="min_tlen" type="integer" value="200" label="Minimum assembled transcript length" />
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52 <param name="min_anchor_len" type="integer" value="10" label="Minimum anchor length for junctions" />
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53 <param name="min_anchor_cov" type="integer" value="1" label="Minimum junction coverage" />
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54 <param name="min_bundle_cov" type="integer" value="2" label="Minimum bundle reads per bp coverage to consider for assembly" />
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55 <param name="maxcov" type="integer" value="1000000" label="Coverage saturation threshold" />
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56 <param name="bdist" type="integer" value="50" label="Gap between read mappings triggering a new bundle" />
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57 <param name="bundle_fraction" type="float" value="0.95" label="Fraction of bundle allowed to be covered by multi-hit reads" />
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58 </when>
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59 </conditional>
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60 </inputs>
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61 <outputs>
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62 <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/>
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63 <data name="coverage" format="gff3" label="${tool.name} on ${on_string}: Coverage">
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64 <filter>guide['use_guide'] == "yes"</filter>
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65 </data>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
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70 <param name="use_guide" value="no" />
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71 <param name="options" value="default" />
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72 <output name="output_gtf" file="stringtie_out1.gtf" ftype="gtf" />
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73 </test>
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74 <test>
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75 <param name="input_bam" value="stringtie_in1.bam" ftype="bam" />
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76 <param name="use_guide" value="no" />
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77 <param name="options" value="advanced" />
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78 <param name="fraction" value="0.17" />
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79 <output name="output_gtf" file="stringtie_out2.gtf" ftype="gtf" />
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80 </test>
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81 </tests>
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82 <help>
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83 <![CDATA[
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84 StringTie v0.97 usage::
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85
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86 stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gff>] [-p <cpus>]
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87 [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
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88 [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
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89
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90 Assemble RNA-Seq alignments into potential transcripts.
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91
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92 Options:
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93 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
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94 -l name prefix for output transcripts (default: STRG)
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95 -f minimum isoform fraction (default: 0.15)
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96 -m minimum assembled transcript length to report (default 200bp)
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97 -o output file with the assembled transcripts (default: stdout)
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98 -a minimum anchor length for junctions (default: 10)
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99 -j minimum junction coverage (default: 1)
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100 -t disable trimming of predicted transcripts based on coverage (default: trimming enabled)
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101 -c minimum bundle reads per bp coverage to consider for assembly (default: 2)
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102 -s coverage saturation threshold; further read alignments will be
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103 ignored in a region where a local coverage depth of <maxcov>
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104 is reached (default: 1,000,000);
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105 -e abundance estimation only of input transcripts (for -G option)
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106 -g gap between read mappings triggering a new bundle (default: 50)
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107 -S more sensitive run (default: no)
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108 -C output file with all transcripts in reference that are fully
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109 covered by reads
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110 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
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111
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112 ]]>
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113 </help>
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114 </tool>
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