Mercurial > repos > galaxyp > maxquant
diff macros.xml @ 11:d72c96ad9a16 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 726423148e26cfb71958171851ec5ed4c307616e"
| author | galaxyp |
|---|---|
| date | Tue, 15 Jun 2021 07:55:59 +0000 |
| parents | f522c08e900c |
| children | 0839f84def5e |
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--- 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 @@ <?xml version="1.0" ?> <macros> <token name="@VERSION@">1.6.10.43</token> + <token name="@VERSION_PTXQC@">1.0.9</token> <token name="@SUBSTITUTION_RX@">[^\w\-\s\.]</token> - <token name="@TMT10PLEX@"><![CDATA[- [TMT10plex-Lys126C,TMT10plex-Nter126C,0,0,0,0,True] + <token name="@TMT2PLEX@"> + - [TMT2plex-Lys126,TMT2plex-Nter126,0,0,0,0,True] + - [TMT2plex-Lys127,TMT2plex-Nter127,0,0,0,0,True] + </token> + <token name="@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] + </token> + <token name="@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] + </token> + <token name="@TMT10PLEX@"> + - [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] - ]]></token> - + </token> + <token name="@TMT11PLEX@"> + @TMT10PLEX@ + - [TMT11plex-Lys131C,TMT11plex-Nter131C,0,0,0,0,True] + </token> + <token name="@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] + </token> + <token name="@ITRAQ8PLEX@"> + - [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] + </token> + <token name="@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] + </token> <xml name="requirements"> <requirements> <requirement type="package" version="@VERSION@">maxquant</requirement> <requirement type="package" version="3.7">python</requirement> <requirement type="package" version="5.1.2">pyyaml</requirement> - <requirement type="package" version="0.92.6">r-ptxqc</requirement> + <requirement type="package" version="@VERSION_PTXQC@">r-ptxqc</requirement> <requirement type="package" version="1.32">tar</requirement> </requirements> </xml> - <xml name="ptxqc"> <configfile name="qr_yaml"> PTXQC: @@ -119,44 +166,35 @@ </configfile> <configfile name="qr"> 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")) </configfile> </xml> - <xml name="mod_option" token_value="default"> <option value="@VALUE@">@VALUE@</option> </xml> <xml name="default_mod_option" token_value="default"> <option selected="true" value="@VALUE@">@VALUE@</option> </xml> - <xml name="ptxqc-opts"> <conditional name="qc"> - <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" - type="boolean" checked="false"/> + <param name="do_it" label="Generate PTXQC (proteomics quality control pipeline) report? (experimental setting)" type="boolean" checked="false"/> <when value="true"> - <param name="parameters" type="boolean" checked="true" - label="use parameters.txt?" truevalue="yes" falsevalue="no" /> - <param name="summary" type="boolean" checked="true" - label="use summary.txt?" truevalue="yes" falsevalue="no" /> - <param name="proteingroups" type="boolean" checked="true" - label="use proteinGroups.txt?" truevalue="yes" falsevalue="no" /> - <param name="evidence" type="boolean" checked="true" - label="use evidence.txt?" truevalue="yes" falsevalue="no" /> - <param name="msms" type="boolean" checked="true" - label="use msms.txt?" truevalue="yes" falsevalue="no" /> - <param name="msmsscans" type="boolean" checked="true" - label="use msmsScans.txt?" truevalue="yes" falsevalue="no" /> + <param name="parameters" type="boolean" checked="true" label="use parameters.txt?" truevalue="yes" falsevalue="no"/> + <param name="summary" type="boolean" checked="true" label="use summary.txt?" truevalue="yes" falsevalue="no"/> + <param name="proteingroups" type="boolean" checked="true" label="use proteinGroups.txt?" truevalue="yes" falsevalue="no"/> + <param name="evidence" type="boolean" checked="true" label="use evidence.txt?" truevalue="yes" falsevalue="no"/> + <param name="msms" type="boolean" checked="true" label="use msms.txt?" truevalue="yes" falsevalue="no"/> + <param name="msmsscans" type="boolean" checked="true" label="use msmsScans.txt?" truevalue="yes" falsevalue="no"/> </when> <when value="false"/> </conditional> </xml> - <xml name="outputs"> <outputs> <expand macro="output_from_wdir" name="proteinGroups" label="MaxQuant Protein Groups"/> @@ -183,7 +221,6 @@ </data> </outputs> </xml> - <xml name="modification"> <expand macro="mod_option" value="Acetyl (K)"/> <expand macro="mod_option" value="Acetyl (Protein N-term)"/> @@ -601,7 +638,6 @@ <expand macro="mod_option" value="Cysteinyl"/> <expand macro="mod_option" value="Cysteinyl - carbamidomethyl"/> </xml> - <xml name="label"> <expand macro="mod_option" value="Arg6"/> <expand macro="mod_option" value="Arg10"/> @@ -638,7 +674,6 @@ <expand macro="mod_option" value="Leu7"/> <expand macro="mod_option" value="Ile7"/> </xml> - <xml name="proteases"> <expand macro="mod_option" value="Trypsin"/> <expand macro="mod_option" value="Trypsin/P"/> @@ -654,7 +689,6 @@ <expand macro="mod_option" value="Chymotrypsin+"/> <expand macro="mod_option" value="Chymotrypsin"/> </xml> - <xml name="iso_labels"> <expand macro="mod_option" value="iTRAQ4plex-Nter114"/> <expand macro="mod_option" value="iTRAQ4plex-Nter115"/> @@ -741,8 +775,7 @@ <expand macro="mod_option" value="iodoTMT6plex-Cys130"/> <expand macro="mod_option" value="iodoTMT6plex-Cys131"/> </xml> - - <xml name="citations"> + <xml name="citations"> <citations> <citation type="bibtex"> @article{cox2008maxquant, @@ -773,4 +806,4 @@ <citation type="doi">10.1021/acs.jproteome.5b00780</citation> </citations> </xml> -</macros> +</macros> \ No newline at end of file