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Changeset 4:7af419c90f5f (2019-03-28)

Previous changeset 3:226287d75d96 (2018-09-26) Next changeset 5:a96af68dafb2 (2020-05-06)

Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c

modified:
moff.xml

added:
tool-data/ptm_setting_ps.json

diff -r 226287d75d96 -r 7af419c90f5f moff.xml
--- a/moff.xml Wed Sep 26 07:15:36 2018 -0400
+++ b/moff.xml Thu Mar 28 05:25:24 2019 -0400

[

b'@@ -1,7 +1,7 @@\n-<tool id="proteomics_moff" name="moFF" version="@VERSION@.2">\n+<tool id="proteomics_moff" name="moFF" version="@VERSION@.0">\n <description>extracts MS1 intensities from spectrum files</description>\n <macros>\n- <token name="@VERSION@">1.2.1</token>\n+ <token name="@VERSION@">2.0.2</token>\n \n <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data">\n \n@@ -48,20 +48,20 @@\n </when>\n </conditional>\n </xml>\n- <xml name="raw_input_macro" token_allow_multiple="true" token_input_type="data">\n- <conditional name="msms_input">\n- <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">\n- <option value="raw">Thermo RAW file</option>\n- <option value="mzml">mzML</option>\n- </param>\n- <when value="raw">\n- <param argument="--inputraw" type="@INPUT_TYPE@" multiple="@ALLOW_MULTIPLE@" format="raw" label="RAW file(s)"/>\n- </when>\n- <when value="mzml">\n- <param argument="--inputraw" type="@INPUT_TYPE@" multiple="@ALLOW_MULTIPLE@" format="mzml" label="mzML file(s)"/>\n- </when>\n- </conditional>\n- </xml>\n+\t<xml name="filt_matched_peptide">\n+ <conditional name="match_filter">\n+ <param name="filter_flags" type="select" label="Activate filtering of matched peptides">\n+ <option selected="True" value="nofilter">Do not activate</option>\n+ <option value="filter">Filter by flags to exclude or require</option>\n+ </param>\n+ <when value="filter">\n+ <param argument="--sample_size" label="sample_size" type="float" value="0.20" help="percentage of MS2 peptide used to estimated the threshold. Default value: 0.20" />\n+ <param argument="--quantile_thr_filtering" label="-quantile_thr_filtering" type="float" value="0.75" help="quantile value used to compute the filtering threshold for the matched peak"/>\n+ <param argument="--ptm_file" type="data" format="tabular" label="ptm_file" optional= "True" help="load your ptm file in order to overwrite internal method"/>\n+ </when>\n+ <when value="nofilter"/>\n+ </conditional>\n+\t</xml>\n \n <token name="@FORMAT@"><![CDATA[\n #if $task.task_selector != \'mbr\'\n@@ -76,14 +76,14 @@\n ]]></token>\n <token name="@IDENT_INPUT_ARG_MULTIPLE@"><![CDATA[\n ## this is where the ident input gets passed to moff/moff_all/moff_mbr\n- --inputtsv\n+ --tsv_list\n #for $value in $task.ident_input.ident_input_file:\n \'./ident_inputs/$value.element_identifier$format\'\n #end for\n ]]></token>\n <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[\n ## this is where the ident input gets passed to moff/moff_all/moff_mbr\n- --inputtsv \'./ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format\'\n+ --tsv_list \'./ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format\'\n ]]></token>\n <token name="@WRANGLE_IDENT_INPUT_SINGLE@"><![CDATA[\n mkdir ./ident_inputs &&\n@@ -122,23 +122,23 @@\n #end if\n ]]></token>\n <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[\n- --inputraw \'./raws/$task.msms_input.inputraw.element_identifier$format\'\n+ --raw_list \'./raws/$task.msms_input.raw_list.element_identifier$format\'\n ]]></token>\n <token name="@RAW_INPUT_ARG_MULTIPLE@"><![CDATA[\n- '..b' <assert_contents>\n <has_text text="NH2-QVEEAVQSDDK-COOH"/>\n- </assert_contents>\n- </element>\n- <element name="mbr_test2_match">\n- <assert_contents>\n <has_text text="NH2-RDVGINNTVK-COOH"/>\n </assert_contents>\n </element>\n@@ -429,6 +340,7 @@\n </tests>\n <help>\n <![CDATA[\n+\n **Description**\n \n moFF (a Modest Feature Finder) is an OS independent tool designed to extract\n@@ -441,28 +353,24 @@\n \n *Modules:*\n \n-1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file. \n+1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.\n 2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time.\n 3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files.\n \n If both match between runs and apex intensity are desired, it is best to run them both at once (i.e., run the \'All\' module).\n The MBR module is mainly useful for observing the intermediate steps of the algorithm - its outputs are not able to be used as inputs in moFF or in other tools.\n-\n-If quantification of multiple files without MBR is desired, the apex intensity module may be run with multiple files or a dataset collection in batch mode. \n-In either case, moFF must be given the paired files at the same time - thus the best method is to construct a dataset collection in which the raw and identification files are in the same order. \n-\n+If quantification of multiple files without MBR is desired, the apex intensity module may be run with multiple files or a dataset collection in batch mode.\n+In either case, moFF must be given the paired files at the same time - thus the best method is to construct a dataset collection in which the raw and identification files are in the same order.\n \n *Inputs:*\n \n - Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker.\n If it is a generic tabular file, please select the columns corresponding to the required information.\n-\n - MS/MS file: this can either be a Thermo raw file or an mzML file.\n \n A given pair of files must have the *exact* same display name, not including the extension;\n e.g. ``example1.tabular`` and ``example1.mzml``.\n If the display names are different, simply change them in the history menu.\n-\n For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections.\n This allows for usage of the output dataset collections in workflows.\n \n@@ -473,20 +381,16 @@\n For correct rt windows, we suggest you set the ``rt_p`` value equal to or slighly greater than the\n dynamic exclusion duration set in your machine. We suggest also to set the\n ``rt_p_match`` always slightly bigger than tha values used for ``rt_p``.\n-\n *Outputs:*\n-\n When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file,\n and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"),\n the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary.\n-\n If used with a generic tabular format, the only columns in the output file are the 7 columns selected while using moFF plus the columns that moFF adds. Other columns are discarded.\n \n **More Information**\n \n-See the moFF Github site at https://github.com/compomics/moFF, \n-and the publication at https://dx.doi.org/10.1038/nmeth.4075 \n-\n+See the moFF Github site at https://github.com/compomics/moFF,\n+and the publication at https://dx.doi.org/10.1038/nmeth.4075\n ]]>\n </help>\n <citations>\n'

diff -r 226287d75d96 -r 7af419c90f5f tool-data/ptm_setting_ps.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ptm_setting_ps.json Thu Mar 28 05:25:24 2019 -0400

[

@@ -0,0 +1,5 @@
+{
+"<cmm>": {"deltaChem":[3,2,1,1],"desc":"Carboxyamidomethylation C unimod:4"},
+"<ox>": {"deltaChem":[0,0,0,1],"desc":"oxidation oxidation unimod:35" } ,
+"ace-": {"deltaChem":[2,2,0,1],"desc":"Acetylation N-term unimod:1" },
+"pyro-": {"deltaChem":[-3,0,-1,0],"desc":"Pyro-glu from Q unimod:28" }}