ctat_analyze_differential_expression: ctat_analyze_differential

annotate ctat_analyze_differential_expression.xml @ 5:57bdc1772c5b draft default tip

Uploaded

author	trinity_ctat
date	Mon, 02 Jul 2018 11:22:20 -0400
parents	b37d57c8ce7e
children

rev	line source
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	1 <tool id="ctat_analyze_differential_expression" name="ctat_analyze_differential_expression" version="1.0.0" profile="17.05">
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	2
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	3 <description>Analyze differential expression</description>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	4 <requirements>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	5 <requirement type="package" version="2.7">python</requirement>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	6 <requirement type="package">subprocess32</requirement>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	7 <requirement type="package">bzip2</requirement>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	8 <requirement type="package" version="1.3.0">rsem</requirement>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	9 <requirement type="package" version="3">bioconductor-edger</requirement>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	10 <requirement type="package" version="2">bioconductor-qvalue</requirement>
3 68c6c52d2ced Uploaded trinity_ctat parents: 2 diff changeset	11 <requirement type="package">r-cluster</requirement>
68c6c52d2ced Uploaded trinity_ctat parents: 2 diff changeset	12 <requirement type="package">r-fastcluster</requirement>
2 ab08b6af7710 Updating tools requirements. trinity_ctat parents: 1 diff changeset	13 <requirement type="package" version="2.6.6">trinity</requirement>
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	14 </requirements>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	15 <command detect_errors="exit_code">
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	16 <![CDATA[
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	17 python $__tool_directory__/ctat_analyze_differential_expression.py $EdgeRTarGz $Counts_matrix $Pvalue $Cvalue
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	18 ]]>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	19 </command>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	20 <inputs>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	21 <param name="EdgeRTarGz" label="EdgeR tar gz file" type="data" format="txt"/>
3 68c6c52d2ced Uploaded trinity_ctat parents: 2 diff changeset	22 <param name="Counts_matrix" label="Counts Matrix" type="data" format="tabular" />
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	23 <param name="Pvalue" label="P-value" value="0.05" type="float" />
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	24 <param name="Cvalue" label="C-value" value="0" type="float" />
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	25
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	26 </inputs>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	27 <outputs>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	28 <data format="data" name="diffExpr_matrix" label="${tool.name} on ${on_string}: Matrix" from_work_dir="diffExpr.matrix"/>
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	29 <data format="data" name="diffExpr_correlation_matrix" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix" from_work_dir="diffExpr.matrix.log2.sample_cor.dat"/>
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	30 <data format="data" name="diffExpr_correlation_matrix_pdf" label="${tool.name} on ${on_string}: Sample_Correlation_Matrix_PDF" from_work_dir="diffExpr.matrix.log2.sample_cor_matrix.pdf"/>
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	31 <data format="data" name="Heatmap" label="${tool.name} on ${on_string}: Heatmap" from_work_dir="diffExpr.matrix.log2.centered.genes_vs_samples_heatmap.pdf"/>
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	32 </outputs>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	33 <tests>
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	34 <test>
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	35 <param name="EdgeRTarGz" value="Sp.edgeR.tar.gz" ftype="tar" />
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	36 <param name="TMM_Matrix_FPKM" value="Sp.TMM.EXPR.matrix" />
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	37 <param name="Pvalue" value="0.05" />
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	38 <param name="Cvalue" value="0.0" />
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	39
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	40 <output name="diffExpr_matrix" >
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	41 <assert_contents>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	42 <has_line_matching expression=".+" />
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	43 <has_line line="Sp_ds Sp_hs" />
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	44 <has_line_matching expression="TRINITY_DN.+" />
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	45 </assert_contents>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	46 </output>
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	47 <output name="diffExpr_correlation_matrix" file="Sp.diffExpr.matrix.log2.sample_cor.dat" />
b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	48 <output name="diffExpr_correlation_matrix_pdf" >
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	49 <assert_contents>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	50 <has_line_matching expression=".+" />
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	51 </assert_contents>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	52 </output>
4 b37d57c8ce7e Uploaded trinity_ctat parents: 3 diff changeset	53 <output name="Heatmap" >
0 6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	54 <assert_contents>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	55 <has_line_matching expression=".+" />
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	56 </assert_contents>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	57 </output>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	58
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	59 </test>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	60 </tests>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	61 <help>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	62 .. class:: infomark
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	63
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	64 This tool filters differentially expressed transcripts derived from edgeR using a minimum fold change (C-value) which will be log2 transformed before use and a required significance (P-value) in the pairwise sample comparisons (after false discovery rate correction).
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	65
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	66 If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_.
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	67
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	68 .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	69 .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	70 </help>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	71
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	72 <citations>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	73 <citation type="doi">10.1038/nbt.1883</citation>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	74 </citations>
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	75
6a8dadcd45e3 Revamp and renaming of previous tools. Many of tools are new versions. Adding ctat_metagenomics tool. trinity_ctat parents: diff changeset	76 </tool>

Mercurial > repos > trinity_ctat > ctat_analyze_differential_expression

annotate ctat_analyze_differential_expression.xml @ 5:57bdc1772c5b draft default tip