proteomics_moff: moff.xml annotate

annotate moff.xml @ 3:226287d75d96 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97

author	galaxyp
date	Wed, 26 Sep 2018 07:15:36 -0400
parents	28b65ce1a091
children	7af419c90f5f

rev	line source
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.2">
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>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	4 <token name="@VERSION@">1.2.1</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>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	51 <xml name="raw_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	52 <conditional name="msms_input">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	53 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	54 <option value="raw">Thermo RAW file</option>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	55 <option value="mzml">mzML</option>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	56 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	57 <when value="raw">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	58 <param argument="--inputraw" type="@INPUT_TYPE@" multiple="@ALLOW_MULTIPLE@" format="raw" label="RAW file(s)"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	59 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	60 <when value="mzml">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	61 <param argument="--inputraw" type="@INPUT_TYPE@" multiple="@ALLOW_MULTIPLE@" format="mzml" label="mzML file(s)"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	62 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	63 </conditional>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	64 </xml>
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
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	79 --inputtsv
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$format'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	82 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	83 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	84 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	85 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	86 --inputtsv './ident_inputs/${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}$format' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	121 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	122 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	123 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	124 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	125 --inputraw './raws/$task.msms_input.inputraw.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[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	128 --inputraw
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	129 #for $value in $task.msms_input.inputraw:
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	130 './raws/$value.element_identifier$format'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	131 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	132 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	133 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	134 mkdir ./raws &&
3 226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	135 ## for files, need to softlink the name to the history item
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	136 ln -s '$task.msms_input.inputraw' './raws/$task.msms_input.inputraw.element_identifier$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
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	141 #for $value in $task.msms_input.inputraw:
226287d75d96 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	142 ln -s '$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@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	156 moff.py
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
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	160 --rt_w $task.rt_w
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	161 --rt_p $task.rt_p
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	162 --output_folder ./out
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	163 #if ($task.peptide_summary):
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	164 --peptide_summary 1
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	165 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	166 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	167 #if $task.peptide_summary:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	168 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	169 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	170 mv ./out/*moff_result.txt '$output_table'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	171 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	172 mv ./out/*.log '$output_logs'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	173 #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	174 @WRANGLE_IDENT_INPUT_MULTIPLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	175 moff_mbr.py
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	176 --inputF ./ident_inputs
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	177 --ext $task.ext
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	178 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	179 mv ./ident_inputs/mbr_output/* ./out
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	180 #else:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	181 ## moff_all (mbr followed by apex)
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	182 @WRANGLE_IDENT_INPUT_MULTIPLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	183 @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	184 moff_all.py
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	185 @IDENT_INPUT_ARG_MULTIPLE@
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	186 @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	187 --tol $task.tol
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	188 --rt_w $task.rt_w
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	189 --rt_p $task.rt_p
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	190 --rt_p_match $task.rt_p_match
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	191 --output_folder ./out
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	192 #if $task.peptide_summary:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	193 --peptide_summary 1
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	194 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	195 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	196 #if $task.peptide_summary:
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	197 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	198 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	199 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	200 ]]></command>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	201 <inputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	202 <conditional name="task">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	203 <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	204 <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	205 <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	206 <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	207 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	208 <when value = "moff">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	209 <expand macro="ident_input_macro" allow_multiple="false"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	210 <expand macro="raw_input_macro" allow_multiple="false"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	211 <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	212 help="Specify the tolerance parameter in ppm." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	213 <param argument="--rt_w" type="float" value="3.0" label="Retention time window"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	214 help="Specify rt window for xic in minutes." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	215 <param argument="--rt_p" type="float" value="1" label="Time window for the peak"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	216 help="Specify the time windows for the peak in minutes." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	217 <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	218 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	219 <when value="mbr">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	220 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	221 <param argument="--ext" type="text" value="tab" label="Provide the extension used in the display file name (without the period)"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	222 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	223 <when value="all">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	224 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	225 <expand macro="raw_input_macro" allow_multiple="false" input_type="data_collection"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	226 <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	227 help="Specify the tolerance parameter in ppm." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	228 <param argument="--rt_w" type="float" value="3.0" label="Retention time window"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	229 help="Specify rt window for xic in minutes." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	230 <param argument="--rt_p" type="float" value="1" label="Time window for the peak"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	231 help="Specify the time windows for the peak in minutes." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	232 <param argument="--rt_p_match" type="float" value="1.2" label="Time window for the matched peak"
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	233 help="Specify the time windows for the matched peak in minutes." />
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	234 <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	235 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	236 </conditional>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	237 </inputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	238 <outputs>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	239 <data format="tabular" name="output_table" label="${tool.name} on ${on_string}: quantification">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	240 <filter>task['task_selector']=='moff'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	241 </data>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	242 <data format="txt" name="output_logs" label="${tool.name} ${on_string}: log">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	243 <filter>task['task_selector']=='moff'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	244 </data>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	245 <collection name="ident_output" type="list" label="${tool.name} on ${on_string}: quantification">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	246 <filter>task['task_selector']=='all'</filter>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	247 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	248 </collection>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	249 <collection name="ident_output_mbr" type="list" label="${tool.name} on ${on_string}: matched">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	250 <filter>task['task_selector']=='mbr'</filter>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	251 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	252 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	253 <collection name="log_output" type="list" label="${tool.name} on ${on_string}: logs">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	254 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	255 <discover_datasets pattern="(?P<designation>.*)\.log" directory="out" format="txt"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	256 </collection>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	257 <data format="tabular" name="output_peptide_summary" label="${tool.name} on ${on_string}: peptide summary">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	258 <filter>task['peptide_summary'] and (task['task_selector']=='all' or task['task_selector']=='moff')</filter>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	259 </data>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	260 </outputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	261 <tests>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	262 <!-- test moff_all -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	263 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	264 <param name="task\|task_selector" value="all"/>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	265 <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	266 <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	267 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	268 <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	269 <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	270 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	271 </param>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	272 <param name="msms_input\|input_type_selector" value="mzml"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	273 <param name="inputraw">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	274 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	275 <element name="mbr_test1" value="input/mbr_test1.mzml"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	276 <element name="mbr_test2" value="input/mbr_test2.mzml"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	277 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	278 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	279 <param name="peptide_summary" value="true"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	280 <output name="output_peptide_summary" ftype="tabular">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	281 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	282 <has_text text="sumIntensity_mbr_test1"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	283 <has_text text="sumIntensity_mbr_test2"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	284 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	285 </output>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	286 <output_collection name="ident_output" type="list">
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	287 <element name="mbr_test1_match_moff_result">
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	288 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	289 <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	290 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	291 </element>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	292 <element name="mbr_test2_match_moff_result">
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	293 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	294 <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	295 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	296 </element>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	297 </output_collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	298 <output_collection name="log_output" type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	299 <element name="mbr_test1_match__moff">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	300 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	301 <has_line line="peptide at line 200 --> MZ: 783.4200 RT: 134.6997 matched (yes=1/no=0): 0"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	302 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	303 </element>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	304 <element name="mbr_test2_match__moff">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	305 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	306 <has_line line="peptide at line 132 --> MZ: 767.8700 RT: 98.1975 matched (yes=1/no=0): 0"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	307 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	308 </element>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	309 </output_collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	310 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	311 <!-- test moff alone -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	312 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	313 <param name="task\|task_selector" value="moff"/>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	314 <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	315 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	316 <param name="msms_input\|input_type_selector" value="mzml"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	317 <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	318 <param name="peptide_summary" value="true"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	319 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	320 <output name="output_logs">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	321 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	322 <has_line line="peptide at line 294 --> MZ: 677.3300 RT: 60.6078"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	323 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	324 </output>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	325 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	326 <!-- test the generic input -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	327 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	328 <param name="task\|task_selector" value="moff"/>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	329 <param name="ident_input\|input_type_selector" value="generic"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	330 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	331 <param name="remove_header" value="true"/>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	332 <param name="msms_input\|input_type_selector" value="mzml"/>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	333 <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	334 <param name="peptide" value="3"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	335 <param name="prot" value="2"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	336 <param name="mod_peptide" value="7"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	337 <param name="rt" value="13"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	338 <param name="mz" value="14"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	339 <param name="mass" value="17"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	340 <param name="charge" value="15"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	341 <param name="peptide_summary" value="true"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	342 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	343 <output name="output_logs">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	344 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	345 <has_line line="peptide at line 294 --> MZ: 677.3300 RT: 60.6078"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	346 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	347 </output>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	348 </test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	349 <test>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	350 <param name="task\|task_selector" value="all"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	351 <param name="ident_input\|input_type_selector" value="generic"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	352 <param name="ident_input_file">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	353 <collection type="list">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	354 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	355 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	356 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	357 </param>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	358 <param name="remove_header" value="true"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	359 <param name="peptide" value="3"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	360 <param name="prot" value="2"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	361 <param name="mod_peptide" value="7"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	362 <param name="rt" value="13"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	363 <param name="mz" value="14"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	364 <param name="mass" value="17"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	365 <param name="charge" value="15"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	366 <param name="msms_input\|input_type_selector" value="mzml"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	367 <param name="inputraw">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	368 <collection type="list">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	369 <element name="mbr_test1" value="input/mbr_test1.mzml"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	370 <element name="mbr_test2" value="input/mbr_test2.mzml"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	371 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	372 </param>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	373 <param name="peptide_summary" value="true"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	374 <output name="output_peptide_summary" ftype="tabular">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	375 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	376 <has_text text="sumIntensity_mbr_test1"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	377 <has_text text="sumIntensity_mbr_test2"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	378 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	379 </output>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	380 <output_collection name="ident_output" type="list">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	381 <element name="mbr_test1_match_moff_result">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	382 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	383 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	384 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	385 </element>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	386 <element name="mbr_test2_match_moff_result">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	387 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	388 <has_text text="NH2-RDVGINNTVK-COOH"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	389 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	390 </element>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	391 </output_collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	392 <output_collection name="log_output" type="list">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	393 <element name="mbr_test1_match__moff">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	394 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	395 <has_line line="peptide at line 200 --> MZ: 783.4200 RT: 134.6997 matched (yes=1/no=0): 0"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	396 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	397 </element>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	398 <element name="mbr_test2_match__moff">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	399 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	400 <has_line line="peptide at line 132 --> MZ: 767.8700 RT: 98.1975 matched (yes=1/no=0): 0"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	401 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	402 </element>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	403 </output_collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	404 </test>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	405 <!-- test mbr -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	406 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	407 <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	408 <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	409 <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	410 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	411 <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	412 <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	413 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	414 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	415 <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	416 <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	417 <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	418 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	419 <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	420 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	421 </element>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	422 <element name="mbr_test2_match">
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	423 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	424 <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	425 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	426 </element>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	427 </output_collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	428 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	429 </tests>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	430 <help>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	431 <![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	432 Description
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	433
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	434 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	435 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	436 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	437 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	438 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	439
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	440 Usage
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	441
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	442 Modules:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	443
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	444 1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	445 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	446 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	447
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	448 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	449 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.
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	450
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	451 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.
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	452 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.
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	453
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	454
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	455 Inputs:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	456
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	457 - 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	458 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	459
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	460 - 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	461
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	462 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	463 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	464 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	465
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	466 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	467 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	468
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	469 Parameters:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	470
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	471 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	472 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	473 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	474 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	475 ``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	476
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	477 Outputs:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	478
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	479 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	480 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	481 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	482
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	483 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	484
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	485 More Information
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	486
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	487 See the moFF Github site at https://github.com/compomics/moFF,
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	488 and the publication at https://dx.doi.org/10.1038/nmeth.4075
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	489
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	490 ]]>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	491 </help>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	492 <citations>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	493 <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	494 </citations>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	495 </tool>

Mercurial > repos > galaxyp > proteomics_moff

annotate moff.xml @ 3:226287d75d96 draft