proteomics_moff: moff.xml annotate

annotate moff.xml @ 1:5e5c91fab75c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41

author	galaxyp
date	Thu, 18 Jan 2018 00:51:33 -0500
parents	28c4a4a8bbd3
children	132122c34950

rev	line source
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	1 <tool id="proteomics_moff" name="moFF" version="@VERSION@">
28c4a4a8bbd3 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>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	3 <macros>
1 5e5c91fab75c 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 28c4a4a8bbd3 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 -->
28c4a4a8bbd3 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">
28c4a4a8bbd3 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 -->
28c4a4a8bbd3 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">
28c4a4a8bbd3 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:">
28c4a4a8bbd3 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>
28c4a4a8bbd3 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>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	12 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	13 <when value="ps">
28c4a4a8bbd3 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@"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	15 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	16 <when value="generic">
28c4a4a8bbd3 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@"
28c4a4a8bbd3 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. "/>
28c4a4a8bbd3 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"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	20 <param name="peptide"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	21 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	24 <param name="prot"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	25 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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"/>
28c4a4a8bbd3 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"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	29 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	32 <param name="rt"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	33 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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)"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	36 <param name="mz"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	37 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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)"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	40 <param name="mass"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	41 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	44 <param name="charge"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	45 type="data_column"
28c4a4a8bbd3 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"
28c4a4a8bbd3 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"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	48 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	49 </conditional>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	50 </xml>
28c4a4a8bbd3 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">
28c4a4a8bbd3 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">
28c4a4a8bbd3 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">
28c4a4a8bbd3 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>
28c4a4a8bbd3 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>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	56 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	57 <when value="raw">
28c4a4a8bbd3 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)"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	59 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	60 <when value="mzml">
28c4a4a8bbd3 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)"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	62 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	63 </conditional>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	64 </xml>
28c4a4a8bbd3 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>) -->
28c4a4a8bbd3 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[
28c4a4a8bbd3 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
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	68 --inputtsv
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	69 #for $key in $task.ident_input.ident_input_file.keys():
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	70 './ident_inputs/${task.ident_input.ident_input_file[$key].display_name}'
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	71 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	72 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	73 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	74 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	75 --inputtsv './ident_inputs/${task.ident_input.ident_input_file.display_name}'
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	76 ]]></token>
28c4a4a8bbd3 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[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	78 mkdir ./ident_inputs &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	79 #if $task.ident_input.input_type_selector == "ps":
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	80 ln -s '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.display_name' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	81 #else
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	82 ## optionally remove first line
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	83 #if $task.ident_input.remove_header:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	84 sed -i '1d' '$task.ident_input.ident_input_file' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	85 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	86 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	87 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > tempfile.tab &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	88 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="$task.ident_input.charge" '$task.ident_input.ident_input_file' >> tempfile.tab &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	89 mv tempfile.tab '$task.ident_input.ident_input_file' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	90 ln -s '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.display_name' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	91 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	92 ]]></token>
28c4a4a8bbd3 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[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	94 mkdir ./ident_inputs &&
28c4a4a8bbd3 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":
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	96 #for $key in $task.ident_input.ident_input_file.keys():
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	97 ln -s '${task.ident_input.ident_input_file[$key]}' './ident_inputs/${task.ident_input.ident_input_file[$key].display_name}' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	98 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	99 #else
28c4a4a8bbd3 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():
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	101 ## optionally remove first line
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	102 #if $task.ident_input.remove_header:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	103 sed -i '1d' '$task.ident_input.ident_input_file[$key]' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	104 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	105 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	106 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > tempfile.tab &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	107 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${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" '$filename' >> tempfile.tab &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	108 mv tempfile.tab '$task.ident_input.ident_input_file[$key]' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	109 ln -s '$task.ident_input.ident_input_file[$key]' './ident_inputs/$task.ident_input.ident_input_file[$key].display_name' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	110 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	111 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	112 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	113 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	114 --inputraw './raws/$task.msms_input.inputraw.display_name'
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	115 ]]></token>
28c4a4a8bbd3 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[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	117 --inputraw
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	118 #for $key in $task.msms_input.inputraw.keys():
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	119 './raws/$task.msms_input.inputraw[$key].display_name'
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	120 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	121 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	122 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	123 mkdir ./raws &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	124 ## for files, need to softlink the display name to the history item
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	125 ln -s '$task.msms_input.inputraw' './raws/$task.msms_input.inputraw.display_name' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	126 ]]></token>
28c4a4a8bbd3 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[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	128 mkdir ./raws &&
28c4a4a8bbd3 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
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	130 #for $key in $task.msms_input.inputraw.keys():
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	131 ln -s '$task.msms_input.inputraw[$key]' './raws/$task.msms_input.inputraw[$key].display_name' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	132 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	133 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	134 </macros>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	135 <requirements>
28c4a4a8bbd3 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>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	137 </requirements>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	138 <command detect_errors="aggressive"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	139 mkdir ./out &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	140 #if $task.task_selector == "moff":
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	141 @WRANGLE_IDENT_INPUT_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	142 @WRANGLE_RAW_INPUT_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	143 moff.py
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	144 @IDENT_INPUT_ARG_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	145 @RAW_INPUT_ARG_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	146 --tol $task.tol
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	147 --rt_w $task.rt_w
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	148 --rt_p $task.rt_p
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	149 --output_folder ./out
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	150 #if ($task.peptide_summary):
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	151 --peptide_summary 1
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	152 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	153 &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	154 #if $task.peptide_summary:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	155 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	156 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	157 mv ./out/*moff_result.txt '$output_table'
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	158 &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	159 mv ./out/*.log '$output_logs'
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	160 #else if $task.task_selector == "mbr":
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	161 @WRANGLE_IDENT_INPUT_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	162 moff_mbr.py
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	163 --inputF ./ident_inputs
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	164 --ext $task.ext
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	165 &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	166 mv ./ident_inputs/mbr_output/* ./out
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	167 #else:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	168 ## moff_all (mbr followed by apex)
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	169 @WRANGLE_IDENT_INPUT_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	170 @WRANGLE_RAW_INPUT_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	171 moff_all.py
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	172 @IDENT_INPUT_ARG_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	173 @RAW_INPUT_ARG_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	174 --tol $task.tol
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	175 --rt_w $task.rt_w
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	176 --rt_p $task.rt_p
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	177 --rt_p_match $task.rt_p_match
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	178 --output_folder ./out
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	179 #if $task.peptide_summary:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	180 --peptide_summary 1
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	181 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	182 &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	183 #if $task.peptide_summary:
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	184 mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	185 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	186 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	187 ]]></command>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	188 <inputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	189 <conditional name="task">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	190 <param name="task_selector" type="select" label="Choose which module to run">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	191 <option value="moff" selected="true">Apex intensity</option>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	192 <option value="mbr">Match between runs</option>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	193 <option value="all">All (match-between-runs followed by quantitation)</option>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	194 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	195 <when value = "moff">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	196 <expand macro="ident_input_macro" allow_multiple="false"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	197 <expand macro="raw_input_macro" allow_multiple="false"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	198 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	199 help="Specify the tolerance parameter in ppm." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	200 <param argument="--rt_w" type="float" value="3.0" label="Retention time window"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	201 help="Specify rt window for xic in minutes." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	202 <param argument="--rt_p" type="float" value="1" label="Time window for the peak"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	203 help="Specify the time windows for the peak in minutes." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	204 <param argument="--rt_p_match" type="float" value="1.5" label="Time window for the matched peak"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	205 help="Specify the time windows for the matched peak in minutes." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	206 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	207 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	208 <when value="mbr">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	209 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	210 <param argument="--ext" type="text" value="tab" label="Provide the extension used in the display file name (without the period)"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	211 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	212 <when value="all">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	213 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	214 <expand macro="raw_input_macro" allow_multiple="false" input_type="data_collection"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	215 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	216 help="Specify the tolerance parameter in ppm." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	217 <param argument="--rt_w" type="float" value="3.0" label="Retention time window"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	218 help="Specify rt window for xic in minutes." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	219 <param argument="--rt_p" type="float" value="1" label="Time window for the peak"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	220 help="Specify the time windows for the peak in minutes." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	221 <param argument="--rt_p_match" type="float" value="1.2" label="Time window for the matched peak"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	222 help="Specify the time windows for the matched peak in minutes." />
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	223 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	224 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	225 </conditional>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	226 </inputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	227 <outputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	228 <data format="tabular" name="output_table" label="${tool.name} quantification: ${on_string}">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	229 <filter>task['task_selector']=='moff'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	230 </data>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	231 <data format="txt" name="output_logs" label="${tool.name} log: ${on_string}">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	232 <filter>task['task_selector']=='moff'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	233 </data>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	234 <collection name="ident_output" type="list" label="${tool.name} quantification: ${on_string}">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	235 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	236 <!--discover datasets method -->
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	237 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	238 </collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	239 <collection name="log_output" type="list" label="${tool.name} logs: ${on_string}">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	240 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	241 <discover_datasets pattern="(?P<designation>.*)\.log" directory="out" format="txt"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	242 </collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	243 <data format="tabular" name="output_peptide_summary" label="${tool.name} peptide summary: ${on_string}">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	244 <filter>task['peptide_summary']</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	245 </data>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	246 </outputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	247 <tests>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	248 <!-- test moff_all -->
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	249 <test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	250 <param name="task_selector" value="all"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	251 <param name="ident_input\|input_type_selector" value="ps"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	252 <param name="ident_input_file">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	253 <collection type="list">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	254 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	255 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	256 </collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	257 </param>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	258 <param name="msms_input\|input_type_selector" value="mzml"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	259 <param name="inputraw">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	260 <collection type="list">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	261 <element name="mbr_test1" value="input/mbr_test1.mzml"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	262 <element name="mbr_test2" value="input/mbr_test2.mzml"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	263 </collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	264 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	265 <param name="peptide_summary" value="true"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	266 <output name="output_peptide_summary" ftype="tabular">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	267 <assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	268 <has_text text="sumIntensity_mbr_test1"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	269 <has_text text="sumIntensity_mbr_test2"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	270 </assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	271 </output>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	272 <output_collection name="ident_output" type="list">
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	273 <element name="mbr_test1_match_moff_result">
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	274 <assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	275 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	276 </assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	277 </element>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	278 <element name="mbr_test2_match_moff_result">
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	279 <assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	280 <has_text text="NH2-RDVGINNTVK-COOH"/>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	281 </assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	282 </element>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	283 </output_collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	284 <output_collection name="log_output" type="list">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	285 <element name="mbr_test1_match__moff">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	286 <assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	287 <has_line line="peptide at line 200 --> MZ: 783.4200 RT: 134.6997 matched (yes=1/no=0): 0"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	288 </assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	289 </element>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	290 <element name="mbr_test2_match__moff">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	291 <assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	292 <has_line line="peptide at line 132 --> MZ: 767.8700 RT: 98.1975 matched (yes=1/no=0): 0"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	293 </assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	294 </element>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	295 </output_collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	296 </test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	297 <!-- test moff alone -->
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	298 <test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	299 <param name="task_selector" value="moff"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	300 <param name="ident_input\|input_type_selector" value="ps"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	301 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	302 <param name="msms_input\|input_type_selector" value="mzml"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	303 <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	304 <param name="peptide_summary" value="true"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	305 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	306 <output name="output_logs">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	307 <assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	308 <has_line line="peptide at line 294 --> MZ: 677.3300 RT: 60.6078"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	309 </assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	310 </output>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	311 </test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	312 <!-- test the generic input -->
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	313 <test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	314 <param name="task_selector" value="moff"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	315 <param name="ident_input\|input_type_selector" value="generic"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	316 <param name="ident_input_file" value="input/test.tabular" ftype="tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	317 <param name="remove_header" value="true"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	318 <param name="msms_input\|input_type_selector" value="mzml"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	319 <param name="inputraw" value="input/test.mzml" ftype="mzml"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	320 <param name="peptide" value="3"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	321 <param name="prot" value="2"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	322 <param name="mod_peptide" value="7"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	323 <param name="rt" value="13"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	324 <param name="mz" value="14"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	325 <param name="mass" value="17"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	326 <param name="charge" value="15"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	327 <param name="peptide_summary" value="true"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	328 <output name="output_peptide_summary" ftype="tabular" file="output2/moff_test_pepsum.tab"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	329 <output name="output_logs">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	330 <assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	331 <has_line line="peptide at line 294 --> MZ: 677.3300 RT: 60.6078"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	332 </assert_contents>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	333 </output>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	334 </test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	335 <!-- test mbr -->
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	336 <test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	337 <param name="task_selector" value="mbr"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	338 <param name="ident_input\|input_type_selector" value="ps"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	339 <param name="ident_input_file">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	340 <collection type="list">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	341 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	342 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	343 </collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	344 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	345 <param name="ext" value="tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	346 <output_collection name="ident_output" type="list" count="2">
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	347 <element name="mbr_test1_match">
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	348 <assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	349 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	350 </assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	351 </element>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	352 <element name="mbr_test2_match">
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	353 <assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	354 <has_text text="NH2-RDVGINNTVK-COOH"/>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	355 </assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	356 </element>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	357 </output_collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	358 </test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	359 </tests>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	360 <help>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	361 <![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	362 Description
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	363
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	364 moFF (a Modest Feature Finder) is an OS independent tool designed to extract
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	365 apex MS1 intensity using a set of identified MS2 peptides.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	366 It currently uses a Go library to directly extract data from Thermo Raw spectrum files,
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	367 eliminating the need for conversions from other formats.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	368 Moreover, moFF also allows one to work directly with mzML files.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	369
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	370 Usage
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	371
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	372 Modules:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	373
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	374 1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	375 2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	376 3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	377
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	378 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).
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	379 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.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	380
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	381
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	382 Inputs:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	383
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	384 - Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	385 If it is a generic tabular file, please select the columns corresponding to the required information.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	386
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	387 - MS/MS file: this can either be a Thermo raw file or an mzML file.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	388
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	389 A given pair of files must have the exact same display name, not including the extension;
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	390 e.g. ``example1.tabular`` and ``example1.mzml``.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	391 If the display names are different, simply change them in the history menu.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	392
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	393 For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	394 This allows for usage of the output dataset collections in workflows.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	395
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	396 Parameters:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	397
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	398 All the parameters related to the the time windows (``rt_w``, ``rt_p``, ``rt_p_match``) are basically the
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	399 half of the entire time windows where the apex peak is searched or the XIC is retrieved.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	400 For correct rt windows, we suggest you set the ``rt_p`` value equal to or slighly greater than the
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	401 dynamic exclusion duration set in your machine. We suggest also to set the
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	402 ``rt_p_match`` always slightly bigger than tha values used for ``rt_p``.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	403
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	404 Outputs:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	405
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	406 When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file,
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	407 and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"),
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	408 the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	409
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	410 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.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	411
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	412 More Information
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	413
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	414 See the moFF Github site at https://github.com/compomics/moFF,
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	415 and the publication at https://dx.doi.org/10.1038/nmeth.4075
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	416
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	417 ]]>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	418 </help>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	419 <citations>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	420 <citation type="doi">10.1038/nmeth.4075</citation>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	421 </citations>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	422 </tool>

Mercurial > repos > galaxyp > proteomics_moff

annotate moff.xml @ 1:5e5c91fab75c draft