# HG changeset patch
# User galaxyp
# Date 1623743759 0
# Node ID d72c96ad9a169893c9710e0ffbf2e3d3f4160817
# Parent f522c08e900c9443cd3bde3b18d6227446191355
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
diff -r f522c08e900c -r d72c96ad9a16 macros.xml
--- a/macros.xml Fri Mar 12 08:41:06 2021 +0000
+++ b/macros.xml Tue Jun 15 07:55:59 2021 +0000
@@ -1,8 +1,32 @@
1.6.10.43
+ 1.0.9
[^\w\-\s\.]
-
+ - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
+ - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
+
+
+ - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]
+ - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
+ - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
+ - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
+ - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
+ - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
+
+
+ - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]
+ - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
+ - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
+ - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
+ - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
+ - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
+ - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
+ - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
+
+
+ - [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True]
- [TMT10plex-Lys127N,TMT10plex-Nter127N,0,0,0,0,True]
- [TMT10plex-Lys127C,TMT10plex-Nter127C,0,0,0,0,True]
- [TMT10plex-Lys128N,TMT10plex-Nter128N,0,0,0,0,True]
@@ -12,18 +36,41 @@
- [TMT10plex-Lys130N,TMT10plex-Nter130N,0,0,0,0,True]
- [TMT10plex-Lys130C,TMT10plex-Nter130C,0,0,0,0,True]
- [TMT10plex-Lys131N,TMT10plex-Nter131N,0,0,0,0,True]
- ]]>
-
+
+
+ @TMT10PLEX@
+ - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
+
+
+ - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
+ - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
+ - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
+ - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
+
+
+ - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
+ @ITRAQ4PLEX@
+ - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
+ - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
+ - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
+
+
+ - [iodoTMT6plex-Cys126,'',0,0,0,0,True]
+ - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
+ - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
+ - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
+ - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
+ - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
+
maxquant
python
pyyaml
- r-ptxqc
+ r-ptxqc
tar
-
PTXQC:
@@ -119,44 +166,35 @@
library(PTXQC)
+ library(data.table)
library(yaml)
library(methods)
args = commandArgs(trailingOnly=TRUE)
yaml_config = yaml.load_file(input = args[1])
- r = createReport('./combined/txt', yaml_config)
+ r = createReport('./combined/txt', yaml_obj=yaml_config)
cat(paste0("\nReport generated as '", r\$report_file, "'\n\n"))
-
-
-
+
-
-
-
-
-
-
+
+
+
+
+
+
-
@@ -183,7 +221,6 @@
-
@@ -601,7 +638,6 @@
-
@@ -638,7 +674,6 @@
-
@@ -654,7 +689,6 @@
-
@@ -741,8 +775,7 @@
-
-
+
@article{cox2008maxquant,
@@ -773,4 +806,4 @@
10.1021/acs.jproteome.5b00780
-
+
\ No newline at end of file
diff -r f522c08e900c -r d72c96ad9a16 maxquant.xml
--- a/maxquant.xml Fri Mar 12 08:41:06 2021 +0000
+++ b/maxquant.xml Tue Jun 15 07:55:59 2021 +0000
@@ -1,4 +1,4 @@
-
+
@@ -63,7 +63,7 @@
>> '$log' 2>&1
#end if
&&
- cp ./combined/txt/report_v0.92.6_combined.pdf '$ptxqc_report'
+ cp './combined/txt/report_v@VERSION_PTXQC@_combined.pdf' '$ptxqc_report'
#end if
#end if
]]>
@@ -178,57 +178,28 @@
#end for
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
- - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
- - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
+ @TMT2PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
- - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]
- - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
- - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
- - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
- - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
- - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
+ @TMT6PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
- - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]
- - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
- - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
- - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
- - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
- - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
- - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
- - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
+ @TMT8PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
@TMT10PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
- @TMT10PLEX@
- - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
+ @TMT11PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
- - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
- - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
- - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
- - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
+ @ITRAQ4PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
- - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
- - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]
- - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]
- - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]
- - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]
- - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
- - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
- - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
+ @ITRAQ8PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
- - [iodoTMT6plex-Cys126,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
+ @IODOTMT6PLEX@
#end if
#end if
#if $pg.quant_method.select_quant_method == 'reporter_ion_ms3':
@@ -248,58 +219,29 @@
- ['$l.internallabel','$l.terminallabel',$l.cm2,$l.cm1,$l.cp1,$l.cp2,$l.tmtlike]
#end for
#end if
- #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
- - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True]
- - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True]
+ #if $pg.quant_method.iso_labels.labeling == 'tmt2plex':
+ @TMT2PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt6plex':
- - [TMT6plex-Lys126,TMT6plex-Nter126,0,0,0,0,True]
- - [TMT6plex-Lys127,TMT6plex-Nter127,0,0,0,0,True]
- - [TMT6plex-Lys128,TMT6plex-Nter128,0,0,0,0,True]
- - [TMT6plex-Lys129,TMT6plex-Nter129,0,0,0,0,True]
- - [TMT6plex-Lys130,TMT6plex-Nter130,0,0,0,0,True]
- - [TMT6plex-Lys131,TMT6plex-Nter131,0,0,0,0,True]
+ @TMT6PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt8plex':
- - [TMT8plex-Lys126C,TMT8plex-Nter126C,0,0,0,0,True]
- - [TMT8plex-Lys127N,TMT8plex-Nter127N,0,0,0,0,True]
- - [TMT8plex-Lys127C,TMT8plex-Nter127C,0,0,0,0,True]
- - [TMT8plex-Lys128C,TMT8plex-Nter128C,0,0,0,0,True]
- - [TMT8plex-Lys129N,TMT8plex-Nter129N,0,0,0,0,True]
- - [TMT8plex-Lys129C,TMT8plex-Nter129C,0,0,0,0,True]
- - [TMT8plex-Lys130C,TMT8plex-Nter130C,0,0,0,0,True]
- - [TMT8plex-Lys131N,TMT8plex-Nter131N,0,0,0,0,True]
+ @TMT8PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt10plex':
@TMT10PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'tmt11plex':
- @TMT10PLEX@
- - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True]
+ @TMT11PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'itraq4plex':
- - [iTRAQ4plex-Lys114,iTRAQ4plex-Nter114,0,0,0,0,False]
- - [iTRAQ4plex-Lys115,iTRAQ4plex-Nter115,0,0,0,0,False]
- - [iTRAQ4plex-Lys116,iTRAQ4plex-Nter116,0,0,0,0,False]
- - [iTRAQ4plex-Lys117,iTRAQ4plex-Nter117,0,0,0,0,False]
+ @ITRAQ4PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'itraq8plex':
- - [iTRAQ4plex-Lys113,iTRAQ8plex-Nter113,0,0,0,0,False]
- - [iTRAQ4plex-Lys114,iTRAQ8plex-Nter114,0,0,0,0,False]
- - [iTRAQ4plex-Lys115,iTRAQ8plex-Nter115,0,0,0,0,False]
- - [iTRAQ4plex-Lys116,iTRAQ8plex-Nter116,0,0,0,0,False]
- - [iTRAQ4plex-Lys117,iTRAQ8plex-Nter117,0,0,0,0,False]
- - [iTRAQ4plex-Lys118,iTRAQ8plex-Nter118,0,0,0,0,False]
- - [iTRAQ4plex-Lys119,iTRAQ8plex-Nter119,0,0,0,0,False]
- - [iTRAQ4plex-Lys121,iTRAQ8plex-Nter121,0,0,0,0,False]
+ @ITRAQ8PLEX@
#end if
#if $pg.quant_method.iso_labels.labeling == 'iodotmt6plex':
- - [iodoTMT6plex-Cys126,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys127,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys128,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys129,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys130,'',0,0,0,0,True]
- - [iodoTMT6plex-Cys131,'',0,0,0,0,True]
+ @IODOTMT6PLEX@
#end if
#end if
#end for
@@ -554,15 +496,14 @@
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
@@ -591,7 +532,7 @@
max="1"
help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
-
+
@@ -608,15 +549,14 @@
-
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
@@ -645,7 +585,7 @@
max="1"
help="MS/MS spectra with a lower value for the PIF will be discarded for isobaric label quantification."/>
-
+
@@ -663,7 +603,7 @@
-
+
@@ -780,7 +720,7 @@
-
+
@@ -849,7 +789,7 @@
-