Mercurial > repos > iuc > trinity_samples_qccheck

annotate samples_qccheck.xml @ 9:c5cce95aa90a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:10:27 -0400
parents 6ac9b8130aa2
children 001318fc2916
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1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@">
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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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6 <expand macro="requirements">
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7 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
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8 <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
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9 <requirement type="package" version="2.0.6">r-cluster</requirement>
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10 <requirement type="package" version="1.1.24">r-fastcluster</requirement>
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11 </expand>
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12 <command detect_errors="aggressive"><![CDATA[
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14 ln -f -s '${matrix}' "input.matrix"
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16 &&
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18 PtR
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19 --matrix "input.matrix"
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21 --samples '${samples}'
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23 --CPM --log2 --compare_replicates
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25 &&
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27 PtR
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28 --matrix "input.matrix"
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30 --samples '${samples}'
0
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32 --CPM --log2 --sample_cor_matrix
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34 &&
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36 PtR
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37 --matrix "input.matrix"
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39 --samples '${samples}'
0
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41 --CPM --log2 --prin_comp 3
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43 && mkdir out_pdf
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44 && mv *rep_compare.pdf out_pdf/
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45 && mv *sample_cor_matrix.pdf out_pdf/
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46 && mv *principal_components.pdf out_pdf/
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48 ]]></command>
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49 <inputs>
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50 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
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51 <param format="tabular" name="samples" argument="--samples" type="data" label="Samples description" help="file describing samples and replicates"/>
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52 </inputs>
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53 <outputs>
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54 <collection name="reports" type="list" label="Quality check result files on ${on_string}">
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55 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
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56 </collection>
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57 </outputs>
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58 <tests>
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59 <test>
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60 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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61 <param name="samples" value="count/samples.txt"/>
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62 <output_collection name="reports">
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63 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
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64 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
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65 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
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66 <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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67 <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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68 </output_collection>
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69 </test>
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70 </tests>
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71 <help>
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72 <![CDATA[
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73 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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74 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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75
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76 **Inputs**
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78 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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79
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80 You must describe your samples and replicates with a tabular file looking like this:
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81
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82 =========== ================
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83 ConditionA CondA_replicate1
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84 ----------- ----------------
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85 ConditionA CondA_replicate2
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86 ----------- ----------------
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87 ConditionB CondB_replicate1
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88 ----------- ----------------
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89 ConditionB CondB_replicate2
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90 ----------- ----------------
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91 ConditionC CondC_replicate1
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92 ----------- ----------------
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93 ConditionC CondC_replicate2
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94 ----------- ----------------
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95 ConditionC CondC_replicate3
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96 =========== ================
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97
1
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98 This file can be generated with the 'Describe samples and replicates' tool.
0
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99 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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100
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101 **Output**
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102
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103 This tool will produce several PDF files, see the following page for more information:
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104
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105 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
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106
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107
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108 .. _Trinity: http://trinityrnaseq.github.io
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109 ]]>
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110 </help>
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111
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112 <expand macro="citation" />
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113 </tool>