proteomics_moff: moff.xml annotate

annotate moff.xml @ 4:7af419c90f5f draft

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

author	galaxyp
date	Thu, 28 Mar 2019 05:25:24 -0400
parents	226287d75d96
children	a96af68dafb2

rev	line source
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.0">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	2 <description>extracts MS1 intensities from spectrum files</description>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	3 <macros>
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	4 <token name="@VERSION@">2.0.2</token>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	5 <!-- xml macros, used for shared Galaxy parameter inputs -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	8 <conditional name="ident_input">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	10 <option value="ps">Peptide Shaker PSM report (standard, not extended)</option>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	11 <option value="generic">Another tabular identification file</option>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	12 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	13 <when value="ps">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	14 <param name="ident_input_file" type="@INPUT_TYPE@" format="tabular" label="Peptide Shaker PSM report" multiple="@ALLOW_MULTIPLE@"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	15 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	16 <when value="generic">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	17 <param name="ident_input_file" type="@INPUT_TYPE@" format="tabular" label="A general tabular format" multiple="@ALLOW_MULTIPLE@"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	18 help="Must have specific columns; see below to select these columns from your file. The file should have at most one header line. "/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	19 <param name="remove_header" type="boolean" value="false" label="Remove the header line?" help="This is necessary if the file has a line with column headers"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	20 <param name="peptide"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	21 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	22 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	23 label="Column with peptide-spectrum-match sequence"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	24 <param name="prot"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	25 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	26 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	27 label="Column with protein ID"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	28 <param name="mod_peptide"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	29 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	30 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	31 label="Column with peptide-spectrum-match sequence that contains possible modifications"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	32 <param name="rt"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	33 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	34 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	35 label="Column with PSM retention time (in second)"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	36 <param name="mz"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	37 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	38 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	39 label="Column with m/z (mass over charge)"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	40 <param name="mass"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	41 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	42 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	43 label="Column with mass of the peptide"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	44 <param name="charge"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	45 type="data_column"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	46 data_ref="ident_input_file"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	47 label="Column with charge of ionized peptide"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	48 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	49 </conditional>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	50 </xml>
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	51 <xml name="filt_matched_peptide">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	52 <conditional name="match_filter">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	53 <param name="filter_flags" type="select" label="Activate filtering of matched peptides">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	54 <option selected="True" value="nofilter">Do not activate</option>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	55 <option value="filter">Filter by flags to exclude or require</option>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	56 </param>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	57 <when value="filter">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	58 <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" />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	59 <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"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	60 <param argument="--ptm_file" type="data" format="tabular" label="ptm_file" optional= "True" help="load your ptm file in order to overwrite internal method"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	61 </when>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	62 <when value="nofilter"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	63 </conditional>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	64 </xml>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	65 <!-- tokens (code snippets used in <command>) -->
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	66 <token name="@FORMAT@"><![CDATA[
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	67 #if $task.task_selector != 'mbr'
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	68 #if $task.msms_input.input_type_selector == "raw":
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	69 #set $format = '.raw'
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	70 #else
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	71 #set $format = '.mzml'
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	72 #end if
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	73 #else:
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	74 #set $format = '.tabular'
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	75 #end if
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	76 ]]></token>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	77 <token name="@IDENT_INPUT_ARG_MULTIPLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	78 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	79 --tsv_list
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	80 #for $value in $task.ident_input.ident_input_file:
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	81 './ident_inputs/$value.element_identifier$format'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	82 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	83 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	84 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	85 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	86 --tsv_list './ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	87 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	88 <token name="@WRANGLE_IDENT_INPUT_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	89 mkdir ./ident_inputs &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	90 #if $task.ident_input.input_type_selector == "ps":
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	91 cp '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	92 #else
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	93 cp '$task.ident_input.ident_input_file' ./tempfile1.tab &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	94 ## optionally remove first line
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	95 #if $task.ident_input.remove_header:
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	96 sed -i '1d' ./tempfile1.tab &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	97 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	98 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	99 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > ./tempfile2.tab &&
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	100 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" ./tempfile1.tab >> ./tempfile2.tab &&
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	101 mv ./tempfile2.tab './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	102 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	103 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	104 <token name="@WRANGLE_IDENT_INPUT_MULTIPLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	105 mkdir ./ident_inputs &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	106 #if $task.ident_input.input_type_selector == "ps":
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	107 #for $value in $task.ident_input.ident_input_file:
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	108 cp '${value}' './ident_inputs/${value.element_identifier}$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	109 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	110 #else
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	111 #for $i, $value in enumerate($task.ident_input.ident_input_file):
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	112 cp '${value}' './tempfile${i}_1.tab' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	113 ## optionally remove first line
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	114 #if $task.ident_input.remove_header:
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	115 sed -i '1d' './tempfile${i}_1.tab' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	116 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	117 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	118 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > './tempfile${i}_2.tab' &&
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	119 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" './tempfile${i}_1.tab' >> './tempfile${i}_2.tab' &&
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	120 mv './tempfile${i}_2.tab' './ident_inputs/${value.element_identifier}$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	121 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	122 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	123 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	124 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	125 --raw_list './raws/$task.msms_input.raw_list.element_identifier$format'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	126 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	127 <token name="@RAW_INPUT_ARG_MULTIPLE@"><![CDATA[
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	128 --raw_list
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	129 #for $value in $task.msms_input.raw_list:
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	130 './raws/$value.element_identifier$format'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	131 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	132 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	133 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	134 mkdir ./raws &&
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	135 ## for files, need to softlink the name to the history item
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	136 ln -s '$task.msms_input.raw_list' './raws/$task.msms_input.raw_list.element_identifier$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	137 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	138 <token name="@WRANGLE_RAW_INPUT_MULTIPLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	139 mkdir ./raws &&
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	140 ## for files, need to softlink the name to the history item
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	141 #for $value in $task.msms_input.raw_list:
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	142 ln -s '$value' './raws/$value.element_identifier$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	143 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	144 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	145 </macros>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	146 <requirements>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	147 <requirement type="package" version="@VERSION@">moff</requirement>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	148 </requirements>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	149 <version_command>echo @VERSION@</version_command>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	150 <command detect_errors="aggressive"><![CDATA[
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	151 @FORMAT@
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	152 mkdir ./out &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	153 #if $task.task_selector == "moff":
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	154 @WRANGLE_IDENT_INPUT_SINGLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	155 @WRANGLE_RAW_INPUT_SINGLE@
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	156 moff_all.py
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	157 @IDENT_INPUT_ARG_SINGLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	158 @RAW_INPUT_ARG_SINGLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	159 --tol $task.tol
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	160 --mbr $task.mbr
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	161 --xic_length $task.xic_length
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	162 --rt_peak_win $task.rt_peak_win
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	163 --rt_peak_win_match $task.rt_peak_win_match
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	164 --loc_out ./out
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	165 #if str( $task.match_filter.filter_flags ) == "filter":
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	166 --match_filter
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	167 --sample_size $task.match_filter.sample_size
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	168 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	169 #if ($task.match_filter.ptm_file):
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	170 --ptm_file '$task.match_filter.ptm_file'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	171 #else:
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	172 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	173 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	174 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	175 #if ($task.peptide_summary):
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	176 --peptide_summary
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	177 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	178 #if $task.peptide_summary:
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	179 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	180 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	181 &&
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	182 mv ./out/*moff_result.txt '$output_table'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	183 &&
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	184 mv ./out/*.log '$output_logs'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	185 #else if $task.task_selector == "mbr":
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	186 @WRANGLE_IDENT_INPUT_MULTIPLE@
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	187 moff_all.py
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	188 @IDENT_INPUT_ARG_MULTIPLE@
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	189 --mbr $task.mbr
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	190 --raw_list
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	191 &&
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	192 mv ./mbr_output/* ./out
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	193 #else:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	194 ## moff_all (mbr followed by apex)
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	195 @WRANGLE_IDENT_INPUT_SINGLE@
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	196 @WRANGLE_RAW_INPUT_MULTIPLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	197 moff_all.py
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	198 @IDENT_INPUT_ARG_SINGLE@
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	199 @RAW_INPUT_ARG_MULTIPLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	200 --tol $task.tol
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	201 --mbr $task.mbr
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	202 --xic_length $task.xic_length
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	203 --rt_peak_win $task.rt_peak_win
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	204 --rt_peak_win_match $task.rt_peak_win_match
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	205 --loc_out ./out
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	206 #if ($task.peptide_summary):
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	207 --peptide_summary
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	208 #end if
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	209 #if str( $task.match_filter.filter_flags ) == "filter":
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	210 --match_filter
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	211 --sample_size $task.match_filter.sample_size
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	212 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	213 #if ($task.match_filter.ptm_file):
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	214 --ptm_file '$task.match_filter.ptm_file'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	215 #else:
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	216 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	217 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	218 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	219
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	220 #if $task.peptide_summary:
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	221 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	222 #end if
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	223 #end if
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	224 ]]></command>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	225 <inputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	226 <conditional name="task">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	227 <param name="task_selector" type="select" label="Choose which module to run">
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	228 <option value="moff">Apex intensity</option>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	229 <option value="mbr">Match between runs</option>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	230 <option value="all">All (match-between-runs followed by quantitation)</option>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	231 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	232 <when value = "moff">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	233 <expand macro="ident_input_macro" allow_multiple="false"/>
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	234 <conditional name="msms_input">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	235 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	236 <option value="raw">Thermo RAW file</option>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	237 <option value="mzml">mzML</option>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	238 </param>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	239 <when value="raw">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	240 <param argument="--raw_list" type="data" multiple="false" format="thermo.raw" label="RAW file(s)"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	241 </when>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	242 <when value="mzml">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	243 <param argument="--raw_list" type="data" multiple="false" format="mzml" label="mzML file(s)"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	244 </when>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	245 </conditional>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	246
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	247
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	248 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	249 help="Specify the tolerance parameter in ppm." />
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	250 <param argument="--mbr" type="text" value="off" label="moFF workflow"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	251 help="select the moFF workflow" />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	252 <param argument="--xic_length" type="float" value="3.0" label="retention time windows for XiC"
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	253 help="Specify rt window for xic in minutes." />
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	254 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	255 help="Specify rt window for the peak in minutes." />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	256 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	257 help="Specify the retention time window for the matched peak in minutes." />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	258 <expand macro="filt_matched_peptide"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	259 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	260 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	261 <when value="mbr">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	262 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	263 <param argument="--mbr" type="text" value="only" label="moFF workflow"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	264 help="select the moFF workflow" />
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	265 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	266 <when value="all">
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	267 <expand macro="ident_input_macro" allow_multiple="false" input_type="data"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	268 <conditional name="msms_input">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	269 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	270 <option value="raw">Thermo RAW file</option>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	271 <option value="mzml">mzML</option>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	272 </param>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	273 <when value="raw">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	274 <param argument="--raw_list" type="data" multiple="true" min="2" format="thermo.raw" label="RAW file(s)"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	275 </when>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	276 <when value="mzml">
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	277 <param argument="--raw_list" type="data" multiple="true" min="2" format="mzml" label="mzML file(s)"/>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	278 </when>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	279 </conditional>
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	280
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	281 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	282 help="Specify the tolerance parameter in ppm." />
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	283 <param argument="--mbr" type="text" value="on" label="moFF workflow"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	284 help="select the moFF workflow" />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	285 <param argument="--xic_length" type="float" value="3.0" label="retention time windows for XiC"
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	286 help="Specify rt window for xic in minutes." />
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	287 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	288 help="Specify the retention time window for the peak in minutes." />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	289 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	290 help="Specify the retention time window for the matched peak in minutes." />
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	291 <expand macro="filt_matched_peptide"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	292 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	293 </when>
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	294 </conditional>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	295 </inputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	296 <outputs>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	297 <data format="tabular" name="output_table" label="${tool.name} on ${on_string}: quantification">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	298 <filter>task['task_selector']=='moff'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	299 </data>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	300 <data format="txt" name="output_logs" label="${tool.name} ${on_string}: log">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	301 <filter>task['task_selector']=='moff'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	302 </data>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	303 <collection name="ident_output" type="list" label="${tool.name} on ${on_string}: quantification">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	304 <filter>task['task_selector']=='all'</filter>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	305 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	306 </collection>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	307 <collection name="ident_output_mbr" type="list" label="${tool.name} on ${on_string}: matched">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	308 <filter>task['task_selector']=='mbr'</filter>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	309 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	310 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	311 <collection name="log_output" type="list" label="${tool.name} on ${on_string}: logs">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	312 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	313 <discover_datasets pattern="(?P<designation>.*)\.log" directory="out" format="txt"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	314 </collection>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	315 <data format="tabular" name="output_peptide_summary" label="${tool.name} on ${on_string}: peptide summary">
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	316 <filter>(task['task_selector']=='all' or task['task_selector']=='moff') and task['peptide_summary'] </filter>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	317 </data>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	318 </outputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	319 <tests>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	320 <!-- test mbr -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	321 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	322 <param name="task\|task_selector" value="mbr"/>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	323 <param name="ident_input\|input_type_selector" value="ps"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	324 <param name="ident_input_file">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	325 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	326 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	327 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	328 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	329 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	330 <param name="ext" value="tabular"/>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	331 <output_collection name="ident_output_mbr" type="list" count="2">
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	332 <element name="mbr_test1_match">
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	333 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	334 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	335 <has_text text="NH2-RDVGINNTVK-COOH"/>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	336 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	337 </element>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	338 </output_collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	339 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	340 </tests>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	341 <help>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	342 <![CDATA[
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	343
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	344 Description
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	345
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	346 moFF (a Modest Feature Finder) is an OS independent tool designed to extract
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	347 apex MS1 intensity using a set of identified MS2 peptides.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	348 It currently uses a Go library to directly extract data from Thermo Raw spectrum files,
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	349 eliminating the need for conversions from other formats.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	350 Moreover, moFF also allows one to work directly with mzML files.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	351
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	352 Usage
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	353
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	354 Modules:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	355
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	356 1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	357 2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	358 3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	359
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	360 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).
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	361 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.
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	362 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.
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	363 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.
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	364
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	365 Inputs:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	366
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	367 - Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	368 If it is a generic tabular file, please select the columns corresponding to the required information.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	369 - MS/MS file: this can either be a Thermo raw file or an mzML file.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	370
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	371 A given pair of files must have the exact same display name, not including the extension;
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	372 e.g. ``example1.tabular`` and ``example1.mzml``.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	373 If the display names are different, simply change them in the history menu.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	374 For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	375 This allows for usage of the output dataset collections in workflows.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	376
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	377 Parameters:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	378
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	379 All the parameters related to the the time windows (``rt_w``, ``rt_p``, ``rt_p_match``) are basically the
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	380 half of the entire time windows where the apex peak is searched or the XIC is retrieved.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	381 For correct rt windows, we suggest you set the ``rt_p`` value equal to or slighly greater than the
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	382 dynamic exclusion duration set in your machine. We suggest also to set the
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	383 ``rt_p_match`` always slightly bigger than tha values used for ``rt_p``.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	384 Outputs:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	385 When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file,
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	386 and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"),
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	387 the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	388 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.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	389
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	390 More Information
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	391
4 7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	392 See the moFF Github site at https://github.com/compomics/moFF,
7af419c90f5f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit e6392f9c9e5ff88b1711667305c59b15a751758c galaxyp parents: 3 diff changeset	393 and the publication at https://dx.doi.org/10.1038/nmeth.4075
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	394 ]]>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	395 </help>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	396 <citations>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	397 <citation type="doi">10.1038/nmeth.4075</citation>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	398 </citations>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	399 </tool>

Mercurial > repos > galaxyp > proteomics_moff

annotate moff.xml @ 4:7af419c90f5f draft