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annotate stringtie_merge.xml @ 28:9b48a7386627 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 12bd91ad0bc0a6471f34d1dd342c943f222a17d2
author iuc
date Mon, 30 Jan 2023 12:01:07 +0000
parents d8424a4f39ed
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93404dcc9c96 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit a586aaa6ef561527cda9e922a2260aa591f43938"
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1 <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
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2 <description>transcripts</description>
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3 <xrefs>
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4 <xref type="bio.tools">stringtie</xref>
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5 </xrefs>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="stdio" />
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11 <expand macro="version_command" />
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12 <command><![CDATA[
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13 stringtie --merge
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14 -p \${GALAXY_SLOTS:-1}
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15 #if $guide_gff:
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16 -G '$guide_gff'
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17 #end if
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18 -m $min_len
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19 -c $min_cov
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20 -F $min_fpkm
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21 -T $min_tpm
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22 -f $min_iso
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23 -g $gap_len
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24 $keep_introns
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25 #set inputs = "' '".join(str($input_gtf).split(','))
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26 -o '$out_gtf' '$inputs'
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27 ]]></command>
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28 <inputs>
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29 <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
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30 <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
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31 <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" />
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32 <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" />
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33 <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" />
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34 <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" />
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35 <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
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36 <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" />
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37 <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
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38 </inputs>
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39 <outputs>
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40 <data name="out_gtf" format="gtf" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
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45 <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
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46 <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/>
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47 </test>
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48 <test>
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49 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
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50 <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
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51 <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/>
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52 </test>
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53 <test>
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54 <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
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55 <output name="out_gtf" ftype="gtf">
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56 <assert_contents>
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57 <has_text text="stringtie --merge" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does?**
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64
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65 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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66
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67 If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts.
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69 .. _StringTie: http://ccb.jhu.edu/software/stringtie/
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70 ]]></help>
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71 <expand macro="citations" />
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72 </tool>