Mercurial > repos > iuc > trinity_samples_qccheck

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:11:17 +0000
parents 1b1a25f93f80
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1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>for transcript quantification</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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50ba95fec4a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9
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10 ln -f -s '${matrix}' input.matrix
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11 &&
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12 PtR
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13 --matrix input.matrix
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14 --samples '${samples}'
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15 --CPM --log2 --compare_replicates
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16 &&
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17 PtR
19
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18 --matrix input.matrix
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19 --samples '${samples}'
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20 --CPM --log2 --sample_cor_matrix
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21 &&
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22 PtR
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23 --matrix input.matrix
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24 --samples '${samples}'
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25 --CPM --log2
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26 --prin_comp 3
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27 && mkdir out_pdf
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28 && mv *rep_compare.pdf out_pdf/
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29 && mv *sample_cor_matrix.pdf out_pdf/
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30 && mv *principal_components.pdf out_pdf/
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31
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32 ]]></command>
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33 <inputs>
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34 <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="Output of abundance_estimates_to_matrix tool"/>
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35 <param argument="--samples" format="tabular" type="data" label="Samples description" help="File describing samples and replicates"/>
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36 </inputs>
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37 <outputs>
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38 <collection name="reports" type="list" label="Quality check result files on ${on_string}">
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39 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
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40 </collection>
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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="matrix" value="count/qcheck/matrix.counts.matrix" ftype="tabular" />
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45 <param name="samples" value="count/samples.txt" ftype="tabular"/>
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46 <output_collection name="reports">
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47 <element name="input.matrix.CPM.log2.prcomp.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf"/>
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48 <element name="input.matrix.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf"/>
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49 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
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50 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
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51 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
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52 </output_collection>
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53 </test>
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54 </tests>
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55 <help>
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56 <![CDATA[
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57 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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58 This tool performs some Quality Checks on a RNASeq experiment, analysing the abundance estimation for different samples using a transcriptome assembled with Trinity.
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59
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60 **Inputs**
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62 This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.
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63
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64 You must describe your samples and replicates with a tabular file looking like this:
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65
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66 =========== ================
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67 ConditionA CondA_replicate1
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68 ----------- ----------------
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69 ConditionA CondA_replicate2
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70 ----------- ----------------
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71 ConditionB CondB_replicate1
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72 ----------- ----------------
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73 ConditionB CondB_replicate2
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74 ----------- ----------------
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75 ConditionC CondC_replicate1
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76 ----------- ----------------
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77 ConditionC CondC_replicate2
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78 ----------- ----------------
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79 ConditionC CondC_replicate3
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80 =========== ================
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81
1
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82 This file can be generated with the 'Describe samples and replicates' tool.
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83 The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.
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84
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85 **Output**
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86
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87 This tool will produce several PDF files, see the following page for more information:
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89 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
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90
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91
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92 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
0
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93 ]]>
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94 </help>
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96 <expand macro="citation" />
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97 </tool>