| Previous changeset 11:4c7ab9995f9e (2018-04-07) Next changeset 13:1de83981d43c (2018-05-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 11f68fe2b872f5abc5b660adb10336b0955fa0ee |
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modified:
diffbind.xml |
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added:
test-data/out_diffbind.tab |
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removed:
test-data/out_diffbind.bed |
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| diff -r 4c7ab9995f9e -r fa56d93f7980 diffbind.xml --- a/diffbind.xml Sat Apr 07 15:45:41 2018 -0400 +++ b/diffbind.xml Thu Apr 19 17:15:53 2018 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="diffbind" name="DiffBind" version="2.6.6.1">\n+<tool id="diffbind" name="DiffBind" version="2.6.6.2">\n <description> differential binding analysis of ChIP-Seq peak data</description>\n <requirements>\n <requirement type="package" version="2.6.6">bioconductor-diffbind</requirement>\n@@ -17,7 +17,7 @@\n <regex match="Error in"\n source="both"\n level="fatal"\n- description="An undefined error occured, please check your intput carefully and contact your administrator." />\n+ description="An undefined error occured, please check your input carefully and contact your administrator." />\n </stdio>\n <version_command><![CDATA[\n echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\\$otherPkgs\\$DiffBind\\$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: ")\n@@ -65,7 +65,7 @@\n #end for\n \n $temp_factor.reverse()\n-$temp_factor_names.append([str($factorName), $temp_factor])\n+$temp_factor_names.append(["Condition", $temp_factor])\n \n \n Rscript \'$__tool_directory__/diffbind.R\'\n@@ -104,26 +104,30 @@\n ]]>\n </command>\n <inputs>\n- <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Condition). One factor must be entered and there must be two or more groups. NOTE: Please only use letters, numbers or underscores.">\n- <sanitizer>\n- <valid initial="string.letters,string.digits"><add value="_" /></valid>\n- </sanitizer>\n- </param>\n- <repeat name="rep_group" title="Group" min="2" default="2">\n+ <repeat name="rep_group" title="Group" min="2" max="2" default="2">\n <param name="groupName" type="text" label="Name"\n- help="Name of group that the peak files belong to (e.g. Resistant or Responsive). NOTE: Please only use letters, numbers or underscores (case sensitive).">\n- <sanitizer>\n- <valid initial="string.letters,string.digits"><add value="_" /></valid>\n- </sanitizer>\n+ help="Name for the Group that the peak and BAM files belong to e.g. Resistant/Responsive (two Groups in total must be specified for DiffBind). NOTE: Please only use letters, numbers or underscores.">\n+ <sanitizer>\n+ <valid initial="string.letters,string.digits"><add value="_" /></valid>\n+ </sanitizer>\n+ <validator type="empty_field" />\n </param>\n <param name="peaks" type="data" format="bed" multiple="true" label="Peak files" help="Result of your Peak calling experiment"/>\n- <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used for Peak calling."/>\n- <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one."/>\n+ <param name="bamreads" type="data" format="bam" multiple="true" label="Read BAM file" help="Specify the Read BAM file used in the Peak calling."/>\n+ <param name="bamcontrol" type="data" format="bam" multiple="true" optional="True" label="Control BAM file" help="If specifying a control BAM file, all samples are required to specify one, see Help section below."/>\n </repeat>\n \n- <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)"/>\n+ <param name="scorecol" type="integer" min="0" value="8" label="Score Column" help="Column in peak files that contains peak scores. Default: 8 (narrowPeak)">\n+ <sanitizer>\n+ <valid initial="string.digit'..b'bound\n-* **11th**: a multiple testing corrected FDR p-value\n+* **seqnames**: Chromosome name\n+* **start**: Start position of site\n+* **end**: End position of site\n+* **width**: Length of site\n+* **strand**: Strand\n+* **Conc**: Mean read concentration over all the samples (the default calculation uses log2 normalized ChIP read counts with control read counts subtracted)\n+* **Responsive**: Mean concentration over the first (e.g. Responsive) group\n+* **Resistant**: Mean concentration over second (e.g. Resistant) group\n+* **Fold**: Fold shows the difference in mean concentrations between the two groups (e.g. Responsive - Resistant), with a positive value indicating increased binding affinity in the first group and a negative value indicating increased binding affinity in the second group.\n+* **p.value**: P-value confidence measure for identifying these sites as differentially bound\n+* **FDR**: a multiple testing corrected FDR p-value\n \n \n **Binding Affinity Matrix**\n@@ -333,20 +329,20 @@\n \n Example:\n \n- ===== ====== ====== ================ ================ ================ ================\n- CHR START END MCF7_ER_1.bed MCF7_ER_2.bed BT474_ER_1.bed BT474_ER_2.bed\n- ===== ====== ====== ================ ================ ================ ================\n- chr18 111567 112005 137.615208000375 59.878372946728 29.4139375878664 19.9594576489093\n- chr18 189223 189652 19.9594576489093 12.6059732519427 11.5554754809475 23.110950961895\n- chr18 215232 216063 11.5554754809475 15.7574665649284 31.5149331298568 72.4843461986707\n- chr18 311530 312172 17.8584621069189 11.5554754809475 54.6258840917518 43.0704086108043\n- chr18 346464 347342 75.6358395116564 40.9694130688139 21.0099554199046 16.8079643359236\n- chr18 356560 357362 11.5554754809475 14.7069687939332 57.7773774047375 53.5753863207566\n- chr18 371110 372102 8.40398216796182 9.45447993895705 81.9388261376278 82.989323908623\n- chr18 394600 396513 56.7268796337423 43.0704086108043 510.541916703681 438.05757050501\n- chr18 399014 400382 156.524167878289 117.655750351465 558.864814169461 496.885445680743\n- chr18 498906 500200 767.913870597511 278.381909313735 196.443083176108 181.736114382174\n- ===== ====== ====== ================ ================ ================ ================\n+ ===== ====== ====== ========= ========= ========== ==========\n+ CHR START END MCF7_ER_1 MCF7_ER_2 BT474_ER_1 BT474_ER_2\n+ ===== ====== ====== ========= ========= ========== ==========\n+ chr18 111567 112005 137.6152 59.87837 29.41393 19.95945\n+ chr18 189223 189652 19.95945 12.60597 11.55547 23.11095\n+ chr18 215232 216063 11.55547 15.75746 31.51493 72.48434\n+ chr18 311530 312172 17.85846 11.55547 54.62588 43.07040\n+ chr18 346464 347342 75.63583 40.96941 21.00995 16.80796\n+ chr18 356560 357362 11.55547 14.70696 57.77737 53.57538\n+ chr18 371110 372102 8.403982 9.454479 81.93882 82.98932\n+ chr18 394600 396513 56.72687 43.07040 510.5419 438.0575\n+ chr18 399014 400382 156.5241 117.6557 558.8648 496.8854\n+ chr18 498906 500200 767.9138 278.3819 196.4430 181.7361\n+ ===== ====== ====== ========= ========= ========== ==========\n \n -----\n \n@@ -404,7 +400,7 @@\n differential binding affinity analysis, which enables binding sites to be identified that\n are statistically significantly differentially bound between sample groups. To accomplish\n this, first a contrast (or contrasts) is established, dividing the samples into groups to\n-be compared. Next the core analysis routines are executed, by default using DESeq2 .\n+be compared. Next the core analysis routines are executed, by default using DESeq2.\n This will assign a p-value and FDR to each candidate binding site indicating confidence\n that they are differentially bound.\n \n' |
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| diff -r 4c7ab9995f9e -r fa56d93f7980 test-data/out_diffbind.bed --- a/test-data/out_diffbind.bed Sat Apr 07 15:45:41 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR -chr18 394600 396513 1914 * 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 -chr18 111567 112005 439 * 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 -chr18 346464 347342 879 * 5 5.77 3.24 2.52 6.51e-06 0.00303 -chr18 399014 400382 1369 * 7.62 7 8.05 -1.04 1.04e-05 0.00364 -chr18 371110 372102 993 * 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 |
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| diff -r 4c7ab9995f9e -r fa56d93f7980 test-data/out_diffbind.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_diffbind.tab Thu Apr 19 17:15:53 2018 -0400 |
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| @@ -0,0 +1,6 @@ +seqnames start end width strand Conc Conc_Responsive Conc_Resistant Fold p.value FDR +chr18 394600 396513 1914 * 7.15 5.55 7.89 -2.35 7.06e-24 9.84e-21 +chr18 111567 112005 439 * 5.71 6.53 3.63 2.89 1.27e-08 8.88e-06 +chr18 346464 347342 879 * 5 5.77 3.24 2.52 6.51e-06 0.00303 +chr18 399014 400382 1369 * 7.62 7 8.05 -1.04 1.04e-05 0.00364 +chr18 371110 372102 993 * 4.63 3.07 5.36 -2.3 8.1e-05 0.0226 |