proteomics_moff: moff.xml annotate

annotate moff.xml @ 2:28b65ce1a091 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c

author	galaxyp
date	Wed, 14 Feb 2018 07:19:47 -0500
parents	8f0e76ad46ef
children	226287d75d96

rev	line source
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.1">
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>) -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	66 <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	67 ## 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	68 --inputtsv
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	69 #for $key in $task.ident_input.ident_input_file.keys():
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	70 './ident_inputs/${task.ident_input.ident_input_file[$key].display_name}'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	71 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	72 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	73 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	74 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	75 --inputtsv './ident_inputs/${task.ident_input.ident_input_file.display_name}'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	76 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	77 <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	78 mkdir ./ident_inputs &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	79 #if $task.ident_input.input_type_selector == "ps":
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	80 cp '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.display_name' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	81 #else
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	82 cp '$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	83 ## 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	84 #if $task.ident_input.remove_header:
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	85 sed -i '1d' ./tempfile1.tab &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	86 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	87 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	88 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > ./tempfile2.tab &&
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	89 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${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 &&
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	90 mv ./tempfile2.tab './ident_inputs/$task.ident_input.ident_input_file.display_name' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	91 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	92 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	93 <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	94 mkdir ./ident_inputs &&
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.input_type_selector == "ps":
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	96 #for $key in $task.ident_input.ident_input_file.keys():
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	97 cp '${task.ident_input.ident_input_file[$key]}' './ident_inputs/${task.ident_input.ident_input_file[$key].display_name}' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	98 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	99 #else
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	100 #for $key in $task.ident_input.ident_input_file.keys():
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	101 cp '${task.ident_input.ident_input_file[$key]}' './tempfile${key}_1.tab' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	102 ## 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	103 #if $task.ident_input.remove_header:
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	104 sed -i '1d' './tempfile${key}_1.tab' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	105 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	106 ## 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	107 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > './tempfile${key}_2.tab' &&
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	108 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${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${key}_1.tab' >> './tempfile${key}_2.tab' &&
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	109 mv './tempfile${key}_2.tab' './ident_inputs/$task.ident_input.ident_input_file[$key].display_name' &&
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	110 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	111 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	112 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	113 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	114 --inputraw './raws/$task.msms_input.inputraw.display_name'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	115 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	116 <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	117 --inputraw
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	118 #for $key in $task.msms_input.inputraw.keys():
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	119 './raws/$task.msms_input.inputraw[$key].display_name'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	120 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	121 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	122 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	123 mkdir ./raws &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	124 ## for files, need to softlink the display name to the history item
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	125 ln -s '$task.msms_input.inputraw' './raws/$task.msms_input.inputraw.display_name' &&
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="@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	128 mkdir ./raws &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	129 ## for files, need to softlink the display name to the history item
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	130 #for $key in $task.msms_input.inputraw.keys():
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	131 ln -s '$task.msms_input.inputraw[$key]' './raws/$task.msms_input.inputraw[$key].display_name' &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	132 #end for
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	133 ]]></token>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	134 </macros>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	135 <requirements>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	136 <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	137 </requirements>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	138 <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	139 <command detect_errors="aggressive"><![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	140 mkdir ./out &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	141 #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	142 @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	143 @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	144 moff.py
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	145 @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	146 @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	147 --tol $task.tol
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	148 --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	149 --rt_p $task.rt_p
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	150 --output_folder ./out
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	151 #if ($task.peptide_summary):
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	152 --peptide_summary 1
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	153 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	154 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	155 #if $task.peptide_summary:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	156 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	157 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	158 mv ./out/*moff_result.txt '$output_table'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	159 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	160 mv ./out/*.log '$output_logs'
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	161 #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	162 @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	163 moff_mbr.py
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	164 --inputF ./ident_inputs
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	165 --ext $task.ext
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 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	168 #else:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	169 ## 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	170 @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	171 @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	172 moff_all.py
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	173 @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	174 @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	175 --tol $task.tol
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	176 --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	177 --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	178 --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	179 --output_folder ./out
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	180 #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	181 --peptide_summary 1
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	182 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	183 &&
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	184 #if $task.peptide_summary:
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	185 mv ./out/peptide_summary_intensity_moFF_run.tab '$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	186 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	187 #end if
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	188 ]]></command>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	189 <inputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	190 <conditional name="task">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	191 <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	192 <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	193 <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	194 <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	195 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	196 <when value = "moff">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	197 <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	198 <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	199 <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	200 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	201 <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	202 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	203 <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	204 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	205 <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	206 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	207 <when value="mbr">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	208 <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	209 <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	210 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	211 <when value="all">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	212 <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	213 <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	214 <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	215 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	216 <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	217 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	218 <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	219 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	220 <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	221 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	222 <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	223 </when>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	224 </conditional>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	225 </inputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	226 <outputs>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	227 <data format="tabular" name="output_table" label="${tool.name} on ${on_string}: quantification">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	228 <filter>task['task_selector']=='moff'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	229 </data>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	230 <data format="txt" name="output_logs" label="${tool.name} ${on_string}: log">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	231 <filter>task['task_selector']=='moff'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	232 </data>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	233 <collection name="ident_output" type="list" label="${tool.name} on ${on_string}: quantification">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	234 <filter>task['task_selector']=='all'</filter>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	235 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	236 </collection>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	237 <collection name="ident_output_mbr" type="list" label="${tool.name} on ${on_string}: matched">
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	238 <filter>task['task_selector']=='mbr'</filter>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	239 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	240 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	241 <collection name="log_output" type="list" label="${tool.name} on ${on_string}: logs">
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	242 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	243 <discover_datasets pattern="(?P<designation>.*)\.log" directory="out" format="txt"/>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	244 </collection>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	245 <data format="tabular" name="output_peptide_summary" label="${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	246 <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	247 </data>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	248 </outputs>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	249 <tests>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	250 <!-- test moff_all -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	251 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	252 <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	253 <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	254 <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	255 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	256 <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	257 <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	258 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	259 </param>
1 8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	260 <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	261 <param name="inputraw">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	262 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	263 <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	264 <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	265 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	266 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	267 <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	268 <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	269 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	270 <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	271 <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	272 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	273 </output>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	274 <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	275 <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	276 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	277 <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	278 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	279 </element>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	280 <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	281 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	282 <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	283 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	284 </element>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	285 </output_collection>
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="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	287 <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	288 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	289 <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	290 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	291 </element>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	292 <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	293 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	294 <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	295 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	296 </element>
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 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	299 <!-- test moff alone -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	300 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	310 <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	311 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	312 </output>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	313 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	314 <!-- 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	315 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	316 <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	317 <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	318 <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	319 <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	320 <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	321 <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	322 <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	323 <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	324 <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	325 <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	326 <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	327 <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	328 <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	329 <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	330 <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	331 <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	332 <assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	333 <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	334 </assert_contents>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	335 </output>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	336 </test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	337 <test>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	338 <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	339 <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	340 <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	341 <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	342 <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	343 <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	344 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	345 </param>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	346 <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	347 <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	348 <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	349 <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	350 <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	351 <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	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 <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	359 </collection>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	360 </param>
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="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	362 <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	363 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	364 <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	365 <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	366 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	367 </output>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	368 <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	369 <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	370 <assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	371 <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	372 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	373 </element>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	374 <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	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="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	377 </assert_contents>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	378 </element>
28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	379 </output_collection>
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="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	381 <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	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_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	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">
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_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	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 </test>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	393 <!-- test mbr -->
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	394 <test>
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	395 <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	396 <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	397 <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	398 <collection type="list">
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	399 <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	400 <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	401 </collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	402 </param>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	403 <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	404 <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	405 <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	406 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	407 <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	408 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	409 </element>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	410 <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	411 <assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	412 <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	413 </assert_contents>
8f0e76ad46ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	414 </element>
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	415 </output_collection>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	416 </test>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	417 </tests>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	418 <help>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	419 <![CDATA[
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	420 Description
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	421
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	422 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	423 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	424 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	425 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	426 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	427
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	428 Usage
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	429
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	430 Modules:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	431
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	432 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	433 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	434 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	435
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	436 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	437 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	438
2 28b65ce1a091 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	439 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	440 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	441
0 b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	442
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	443 Inputs:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	444
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	445 - 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	446 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	447
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	448 - 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	449
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	450 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	451 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	452 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	453
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	454 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	455 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	456
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	457 Parameters:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	458
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	459 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	460 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	461 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	462 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	463 ``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	464
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	465 Outputs:
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	466
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	467 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	468 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	469 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	470
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	471 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	472
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	473 More Information
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	474
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	475 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	476 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	477
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 </help>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	480 <citations>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	481 <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	482 </citations>
b4098353ee73 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	483 </tool>

Mercurial > repos > galaxyp > proteomics_moff

annotate moff.xml @ 2:28b65ce1a091 draft