Mercurial > repos > iuc > samples_qccheck

annotate samples_qccheck.xml @ 0:d02ec0323dda draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
author iuc
date Wed, 27 Jul 2016 08:42:42 -0400
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
iuc
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1 <tool id="samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.0">
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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2 <description>for transcript quantification</description>
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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3 <macros>
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iuc
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4 <import>macros.xml</import>
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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8 <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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9 </expand>
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10 <expand macro="stdio"/>
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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11 <command><![CDATA[
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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13 ln -s "${matrix}" "input.matrix"
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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15 &&
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17 PtR
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18 --matrix "input.matrix"
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20 --samples "${samples}"
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22 --CPM --log2 --compare_replicates
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24 &&
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26 PtR
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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27 --matrix "input.matrix"
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29 --samples "${samples}"
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31 --CPM --log2 --sample_cor_matrix
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32
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33 &&
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35 PtR
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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36 --matrix "input.matrix"
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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37
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38 --samples "${samples}"
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40 --CPM --log2 --prin_comp 3
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41
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42 && mkdir out_pdf
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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43 && mv *rep_compare.pdf out_pdf/
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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44 && mv *sample_cor_matrix.pdf out_pdf/
d02ec0323dda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit baff3f60cf4a039a74091e24b3453f4499cfaf02
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45 && mv *principal_components.pdf out_pdf/
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46
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47 ]]></command>
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48 <inputs>
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49 <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
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50 <param format="tabular" name="samples" argument="--samples" type="data" label="Samples description" help="file describing samples and replicates"/>
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51 </inputs>
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52 <outputs>
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53 <collection name="reports" type="list" label="Quality check result files on ${on_string}">
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54 <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
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55 </collection>
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
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60 <param name="samples" value="count/samples.txt"/>
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61 <output_collection name="reports">
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62 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
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63 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
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64 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
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65 <element name="input.matrix.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.principal_components.pdf"/>
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66 <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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67 </output_collection>
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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73 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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74
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75 **Inputs**
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76
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77 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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78
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79 You must describe your samples and replicates with a tabular file looking like this:
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80
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81 =========== ================
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82 ConditionA CondA_replicate1
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83 ----------- ----------------
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84 ConditionA CondA_replicate2
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85 ----------- ----------------
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86 ConditionB CondB_replicate1
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87 ----------- ----------------
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88 ConditionB CondB_replicate2
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89 ----------- ----------------
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90 ConditionC CondC_replicate1
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91 ----------- ----------------
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92 ConditionC CondC_replicate2
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93 ----------- ----------------
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94 ConditionC CondC_replicate3
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95 =========== ================
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96
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97 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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98
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99 **Output**
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100
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101 This tool will produce several PDF files, see the following page for more information:
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102
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103 .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates
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104
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105
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106 .. _Trinity: http://trinityrnaseq.github.io
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107 ]]>
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108 </help>
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109
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110 <expand macro="citation" />
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111 </tool>