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annotate stringtie_merge.xml @ 6:d0bb240d7525 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
author iuc
date Wed, 13 Jul 2016 14:48:26 -0400
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6
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1 <tool id="stringtie_merge" name="StringTie" version="0.1.0">
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2 <description>merge transcripts</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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11 stringtie --merge
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12 -p \${GALAXY_SLOTS:-1}
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13 #if str($guide_gff) != "":
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14 -G "$guide_gff"
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15 #end if
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16 -m $min_len
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17 -c $min_cov
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18 -F $min_fpkm
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19 -T $min_tpm
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20 -f $min_iso
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21 -g $gap_len
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22 $keep_introns
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23 #set inputs = '" "'.join(str($input_gtf).split(','))
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24 -o $out_gtf "$inputs"
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25 ]]>
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26 </command>
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27 <inputs>
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28 <param type="data" name="input_gtf" multiple="true" format="gtf,gff3" />
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29 <param type="data" name="guide_gff" optional="True" format="gtf,gff3" />
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30 <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" />
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31 <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" />
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32 <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" />
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33 <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" />
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34 <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" />
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35 <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" />
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36 <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" />
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37 </inputs>
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38 <outputs>
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39 <data name="out_gtf" format="gtf" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
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44 <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" />
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45 <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
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46 </test>
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47 <test>
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48 <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
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49 <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" />
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50 <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" />
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 **What it does?**
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56
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57 This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples.
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58
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59 If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
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60
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61 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
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62
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63 ------
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64
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65 StringTie --merge has the following options::
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66
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67 -G <guide_gff> reference annotation to include in the merging (GTF/GFF3)
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68 -o <out_gtf> output file name for the merged transcripts GTF
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69 (default: stdout)
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70 -m <min_len> minimum input transcript length to include in the merge
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71 (default: 50)
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72 -c <min_cov> minimum input transcript coverage to include in the merge
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73 (default: 0)
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74 -F <min_fpkm> minimum input transcript FPKM to include in the merge
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75 (default: 1.0)
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76 -T <min_tpm> minimum input transcript TPM to include in the merge
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77 (default: 1.0)
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78 -f <min_iso> minimum isoform fraction (default: 0.01)
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79 -g <gap_len> gap between transcripts to merge together (default: 250)
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80 -i keep merged transcripts with retained introns; by default
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81 these are not kept unless there is strong evidence for them
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82 -l <label> name prefix for output transcripts (default: MSTRG)
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83 ]]></help>
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84 <expand macro="citations" />
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85 </tool>