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comparison edger.xml @ 4:4730985c816f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179
author iuc
date Sat, 05 Jan 2019 05:32:33 -0500
parents d79ed3ec25fe
children fb9b9f0f2f06
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3:d79ed3ec25fe 4:4730985c816f
1 <tool id="edger" name="edgeR" version="3.20.7.2"> 1 <tool id="edger" name="edgeR" version="3.22.5">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement> 7 <requirement type="package" version="3.22.5">bioconductor-edger</requirement>
8 <requirement type="package" version="3.34.9">bioconductor-limma</requirement> 8 <requirement type="package" version="3.36.5">bioconductor-limma</requirement>
9 <requirement type="package" version="0.2.15">r-rjson</requirement> 9 <requirement type="package" version="0.2.20">r-rjson</requirement>
10 <requirement type="package" version="1.20.0">r-getopt</requirement> 10 <requirement type="package" version="1.20.2">r-getopt</requirement>
11 <requirement type="package" version="1.4.30">r-statmod</requirement> 11 <requirement type="package" version="1.4.30">r-statmod</requirement>
12 <!-- required for alpha function used with plotMD --> 12 <!-- required for alpha function used with plotMD -->
13 <requirement type="package" version="0.5.0">r-scales</requirement> 13 <requirement type="package" version="1.0.0">r-scales</requirement>
14 </requirements> 14 </requirements>
15 15
16 <version_command><![CDATA[ 16 <version_command><![CDATA[
17 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 17 echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
18 ]]></version_command> 18 ]]></version_command>
349 <output name="outReport" > 349 <output name="outReport" >
350 <assert_contents> 350 <assert_contents>
351 <has_text text="RData" /> 351 <has_text text="RData" />
352 </assert_contents> 352 </assert_contents>
353 </output> 353 </output>
354 <output name="rscript" value="out_rscript.txt"/> 354 <output name="rscript">
355 <assert_contents>
356 <has_text_matching expression="Task run time" />
357 </assert_contents>
358 </output>
355 </test> 359 </test>
356 <!-- Ensure secondary factors work --> 360 <!-- Ensure secondary factors work -->
357 <test> 361 <test>
358 <param name="format" value="matrix" /> 362 <param name="format" value="matrix" />
359 <param name="counts" value="matrix.txt" /> 363 <param name="counts" value="matrix.txt" />
376 <has_text_matching expression="11304.*0.4584" /> 380 <has_text_matching expression="11304.*0.4584" />
377 </assert_contents> 381 </assert_contents>
378 </element> 382 </element>
379 </output_collection> 383 </output_collection>
380 </test> 384 </test>
381 <!-- Ensure factors file input works --> 385 <!-- Ensure factors file with unordered samples works -->
382 <test> 386 <test>
383 <param name="format" value="matrix" /> 387 <param name="format" value="matrix" />
384 <param name="ffile" value="yes" /> 388 <param name="ffile" value="yes" />
385 <param name="finfo" value="factorinfo.txt" /> 389 <param name="finfo" value="factorinfo.txt" />
386 <param name="counts" value="matrix.txt" /> 390 <param name="counts" value="matrix.txt" />
657 11303 2099 1974 2100 1574 1519 1654 661 11303 2099 1974 2100 1574 1519 1654
658 11304 356 312 337 361 397 346 662 11304 356 312 337 361 397 346
659 11305 2528 2438 2493 1762 1942 2027 663 11305 2528 2438 2493 1762 1942 2027
660 ========== ======= ======= ======= ======== ======== ======== 664 ========== ======= ======= ======= ======== ======== ========
661 665
666
667 **Gene Annotations:**
668 Optional input for gene annotations, this can contain more
669 information about the genes than just an ID number. The annotations will
670 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
671
672 Example:
673
674 ========== ========== ===================================================
675 **GeneID** **Symbol** **GeneName**
676 ---------- ---------- ---------------------------------------------------
677 11287 Pzp pregnancy zone protein
678 11298 Aanat arylalkylamine N-acetyltransferase
679 11302 Aatk apoptosis-associated tyrosine kinase
680 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
681 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
682 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
683 ========== ========== ===================================================
684
662 **Factor Information:** 685 **Factor Information:**
663 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors. 686 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
664 687
665 Example: 688 Example:
666 689
667 ========== ============ ========= 690 ========== ============ =========
668 **Sample** **Genotype** **Batch** 691 **Sample** **Genotype** **Batch**
673 Mut1 Mut b1 696 Mut1 Mut b1
674 Mut2 Mut b2 697 Mut2 Mut b2
675 Mut3 Mut b3 698 Mut3 Mut b3
676 ========== ============ ========= 699 ========== ============ =========
677 700
678 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model. 701 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
679 702
680 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas. 703 *Groups:* The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
681 704
682
683 **Gene Annotations:**
684 Optional input for gene annotations, this can contain more
685 information about the genes than just an ID number. The annotations will
686 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool **annotateMyIDs** can be used to obtain annotations for human, mouse, fly and zebrafish.
687
688 Example:
689
690 ========== ========== ===================================================
691 **GeneID** **Symbol** **GeneName**
692 ---------- ---------- ---------------------------------------------------
693 11287 Pzp pregnancy zone protein
694 11298 Aanat arylalkylamine N-acetyltransferase
695 11302 Aatk apoptosis-associated tyrosine kinase
696 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
697 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
698 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
699 ========== ========== ===================================================
700 705
701 **Contrasts of Interest:** 706 **Contrasts of Interest:**
702 The contrasts you wish to make between levels. 707 The contrasts you wish to make between levels.
703 A common contrast would be a simple difference between two levels: "Mut-WT" 708 A common contrast would be a simple difference between two levels: "Mut-WT"
704 represents the difference between the mutant and wild type genotypes. 709 represents the difference between the mutant and wild type genotypes.