Mercurial > repos > iuc > brew3r_r

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
author iuc
date Thu, 03 Oct 2024 22:35:49 +0000
parents 05f8e9d1e8b8
children
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928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
iuc
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1 <tool id="brew3r_r" name="BREW3R.r" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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2 <description>Extend GTF</description>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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3 <macros>
1
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4 <token name="@TOOL_VERSION@">1.0.2</token>
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d3b0390f325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
iuc
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5 <token name="@VERSION_SUFFIX@">1</token>
0
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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6 </macros>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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7 <xrefs>
2
05f8e9d1e8b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 934f4b672e4f21e211a530281a973b61c20035c5
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8 <xref type="bio.tools">brew3r.r</xref>
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928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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9 <xref type="bioconductor">BREW3R.r</xref>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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10 </xrefs>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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11 <requirements>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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12 <!-- <requirement type="package" version="@TOOL_VERSION@">bioconductor-brew3r.r</requirement>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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13 <requirement type="package" version="1.64.0">bioconductor-rtracklayer</requirement>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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14 <requirement type="package" version="1.20.4">r-getopt</requirement> -->
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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15 <container type="docker">lldelisle/brew3r:v2</container>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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16 </requirements>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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17 <required_files>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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18 <include path="brew3r.r_script.R" />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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19 </required_files>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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20 <version_command><![CDATA[
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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21 echo $(R --version | grep version | grep -v GNU)", BREW3R.r version" $(R --vanilla --slave -e "library(BREW3R.r); cat(sessionInfo()\$otherPkgs\$BREW3R.r\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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22 ]]></version_command>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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23 <command detect_errors="exit_code"><![CDATA[
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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24 Rscript '${__tool_directory__}/brew3r.r_script.R'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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25 --gtf_to_extend '$gtf_to_extend'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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26 --gtf_to_overlap '$gtf_to_overlap'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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27 #if '$sup_output' == 'true':
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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28 --sup_output '$output_table'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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29 #end if
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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30 #if str($no_add) != '':
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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31 '$no_add'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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32 #end if
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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33 #if str($exclude_pattern) != '':
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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34 --exclude_pattern '$exclude_pattern'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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35 #end if
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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36 #if str($filter_unstranded) != '':
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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37 '$filter_unstranded'
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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38 #end if
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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39 -o output.gtf
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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40
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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41 ]]></command>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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42 <inputs>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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43 <param argument="--gtf_to_extend" type="data" format="gtf" label="Input gtf file to be extended on 3'" help="Usually coming from public resource." />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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44 <param argument="--gtf_to_overlap" type="data" format="gtf" label="Input gtf file that will be used to extend" help="Coming from StringTie or another public resource." />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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45 <param argument="--sup_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Get a supplementary output table with resolution of overlaps" />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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46 <param argument="--no_add" type="boolean" truevalue="--no_add" falsevalue="" checked="false" label="Do not add new exons" />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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47 <param argument="--exclude_pattern" type="text" value="" label="Do not extend genes with names matching this pattern" help="Leave empty if you want to extend all genes.">
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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48 <sanitizer>
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49 <valid initial="string.printable">
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50 <remove value="'"/>
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51 <remove value="\"/>
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52 </valid>
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53 </sanitizer>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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54 </param>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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55 <param argument="--filter_unstranded" type="boolean" truevalue="--filter_unstranded" falsevalue="" checked="false" label="Filter unstranded intervals that overlaps genes of both strands" help="Recommanded if you used StringTie on unstranded libraries." />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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56 </inputs>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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57 <outputs>
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58 <data name="output" format="gtf" from_work_dir="output.gtf" label="${tool.name} on ${gtf_to_extend.name} and ${gtf_to_overlap.name}: GTF" />
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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59 <data name="output_table" format="tabular" label="${tool.name} on ${gtf_to_extend.name} and ${gtf_to_overlap.name}: overlap resolution">
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60 <filter>sup_output == True</filter>
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61 </data>
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62 </outputs>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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63 <tests>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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64 <test expect_num_outputs="1">
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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65 <param name="gtf_to_extend" value="input.gtf"/>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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66 <param name="gtf_to_overlap" value="second_input.gtf"/>
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67 <output name="output" value="output.gtf" compare="diff" lines_diff="2"/>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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68 </test>
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69 <test expect_num_outputs="1">
3
d3b0390f325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
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70 <param name="gtf_to_extend" value="input_noexonid.gtf"/>
d3b0390f325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
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71 <param name="gtf_to_overlap" value="second_input.gtf"/>
d3b0390f325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
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72 <output name="output">
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73 <assert_contents>
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74 <has_n_lines n="36"/>
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75 <has_text text="BREW3R"/>
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76 </assert_contents>
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77 </output>
d3b0390f325f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit d287d5688e57f4154d5875789e0cd4d5c87f11ce
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78 </test>
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79 <test expect_num_outputs="1">
0
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80 <param name="gtf_to_extend" value="input.gtf"/>
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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81 <param name="gtf_to_overlap" value="second_input.gtf"/>
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82 <param name="no_add" value="true"/>
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83 <output name="output">
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84 <assert_contents>
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85 <has_n_lines n="31"/>
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86 <not_has_text text="BREW3R"/>
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87 </assert_contents>
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88 </output>
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89 </test>
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90 <test expect_num_outputs="1">
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91 <param name="gtf_to_extend" value="input.gtf"/>
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92 <param name="gtf_to_overlap" value="second_input.gtf"/>
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93 <param name="exclude_pattern" value="^Gm"/>
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94 <output name="output">
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95 <assert_contents>
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96 <has_n_lines n="34"/>
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97 <not_has_text text="exon111.ext"/>
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98 </assert_contents>
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99 </output>
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100 </test>
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101 <test expect_num_outputs="1">
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102 <param name="gtf_to_extend" value="input.gtf"/>
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103 <param name="gtf_to_overlap" value="second_input.gtf"/>
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104 <param name="exclude_pattern" value="Gm$"/>
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105 <output name="output" value="output.gtf" compare="diff" lines_diff="2"/>
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106 <assert_command>
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107 <has_text text="--exclude_pattern 'Gm$'"/>
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108 </assert_command>
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109 </test>
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110 <test expect_num_outputs="1">
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111 <param name="gtf_to_extend" value="input.gtf"/>
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112 <param name="gtf_to_overlap" value="second_input.gtf"/>
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113 <param name="filter_unstranded" value="true"/>
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114 <output name="output">
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115 <assert_contents>
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116 <has_n_lines n="36"/>
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117 <not_has_text text="exon121.ext"/>
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118 </assert_contents>
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119 </output>
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120 </test>
1
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121 <test expect_num_outputs="1">
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122 <param name="gtf_to_extend" value="input2.gtf"/>
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123 <param name="gtf_to_overlap" value="second_input2.gtf"/>
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124 <param name="filter_unstranded" value="true"/>
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125 <output name="output" value="output2.gtf" compare="diff" lines_diff="2"/>
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126 </test>
0
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127 </tests>
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128 <help><![CDATA[
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129
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130 .. class:: infomark
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131
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132 **What it does**
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133
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134 This tool extend the annotations existing in an input GTF file in the 3' end using annotations from another input GTF. During the process, it makes sure that there will not be new overlaps between different genes.
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135
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136 Usage
928a52b5c938 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/brew3r_r commit 3e3c47b732510a9ef0b2864b284aa14308e75ab0
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137 .....
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138
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139
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140 **Input**
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141
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142 2 GTF files:
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143 - First one to extend usually comes from a public resource.
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144 - Second one that is used as template may come from a public resource or from StringTie.
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145
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146
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147 **Output**
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148
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149 1 GTF file with all exons from the input GTF where some of them have been extended (the exon_id ends with '.ext') and potentially new exons (the exon_id contains BREW3R).
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150
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151 ]]></help>
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152 <citations>
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153 <citation type="bibtex">
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154 @unpublished{None,
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155 author = {Lucille Lopez-Delisle},
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156 title = {None},
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157 year = {None},
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158 eprint = {None},
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159 url = {https://github.com/lldelisle/BREW3R.r}
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160 }</citation>
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161 </citations>
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162 </tool>