Mercurial > repos > iuc > trinity_samples_qccheck
comparison samples_qccheck.xml @ 9:226663afe49c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
| author | iuc |
|---|---|
| date | Thu, 14 Jun 2018 03:13:56 -0400 |
| parents | 8bec0d476fa0 |
| children | b58468eb4e64 |
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| 8:1812dbc5bb7b | 9:226663afe49c |
|---|---|
| 1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.0"> | 1 <tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@"> |
| 2 <description>for transcript quantification</description> | 2 <description>for transcript quantification</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
| 7 <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> | 7 <requirement type="package" version="2.38.0">bioconductor-biobase</requirement> |
| 8 <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement> | 8 <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement> |
| 9 <requirement type="package" version="2.0.6">r-cluster</requirement> | 9 <requirement type="package" version="2.0.6">r-cluster</requirement> |
| 10 <requirement type="package" version="1.1.24">r-fastcluster</requirement> | |
| 10 </expand> | 11 </expand> |
| 11 <command detect_errors="aggressive"><![CDATA[ | 12 <command detect_errors="aggressive"><![CDATA[ |
| 12 | 13 |
| 13 ln -f -s "${matrix}" "input.matrix" | 14 ln -f -s '${matrix}' "input.matrix" |
| 14 | 15 |
| 15 && | 16 && |
| 16 | 17 |
| 17 PtR | 18 PtR |
| 18 --matrix "input.matrix" | 19 --matrix "input.matrix" |
| 19 | 20 |
| 20 --samples "${samples}" | 21 --samples '${samples}' |
| 21 | 22 |
| 22 --CPM --log2 --compare_replicates | 23 --CPM --log2 --compare_replicates |
| 23 | 24 |
| 24 && | 25 && |
| 25 | 26 |
| 26 PtR | 27 PtR |
| 27 --matrix "input.matrix" | 28 --matrix "input.matrix" |
| 28 | 29 |
| 29 --samples "${samples}" | 30 --samples '${samples}' |
| 30 | 31 |
| 31 --CPM --log2 --sample_cor_matrix | 32 --CPM --log2 --sample_cor_matrix |
| 32 | 33 |
| 33 && | 34 && |
| 34 | 35 |
| 35 PtR | 36 PtR |
| 36 --matrix "input.matrix" | 37 --matrix "input.matrix" |
| 37 | 38 |
| 38 --samples "${samples}" | 39 --samples '${samples}' |
| 39 | 40 |
| 40 --CPM --log2 --prin_comp 3 | 41 --CPM --log2 --prin_comp 3 |
| 41 | 42 |
| 42 && mkdir out_pdf | 43 && mkdir out_pdf |
| 43 && mv *rep_compare.pdf out_pdf/ | 44 && mv *rep_compare.pdf out_pdf/ |
| 60 <param name="samples" value="count/samples.txt"/> | 61 <param name="samples" value="count/samples.txt"/> |
| 61 <output_collection name="reports"> | 62 <output_collection name="reports"> |
| 62 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> | 63 <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> |
| 63 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> | 64 <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> |
| 64 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> | 65 <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> |
| 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"/> | 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"/> |
| 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"/> | 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"/> |
| 67 </output_collection> | 68 </output_collection> |
| 68 </test> | 69 </test> |
| 69 </tests> | 70 </tests> |
| 70 <help> | 71 <help> |