proteomics_moff: moff.xml annotate

annotate moff.xml @ 4:20ded57bc56b draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52"

author	galaxyp
date	Wed, 06 May 2020 18:49:38 +0000
parents	b7512ccf24f6
children

rev	line source
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.0">
0 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>
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	4 <token name="@VERSION@">2.0.3</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>
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	51 <xml name="filt_matched_peptide">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	52 <conditional name="match_filter">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	53 <param name="filter_flags" type="select" label="Activate filtering of matched peptides">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	54 <option selected="True" value="nofilter">Do not activate</option>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	55 <option value="filter">Filter by flags to exclude or require</option>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	56 </param>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	57 <when value="filter">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	58 <param argument="--sample_size" label="sample_size" type="float" value="0.20" help="percentage of MS2 peptide used to estimated the threshold. Default value: 0.20" />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	59 <param argument="--quantile_thr_filtering" label="-quantile_thr_filtering" type="float" value="0.75" help="quantile value used to compute the filtering threshold for the matched peak"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	60 <param argument="--ptm_file" type="data" format="tabular" label="ptm_file" optional= "True" help="load your ptm file in order to overwrite internal method"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	61 </when>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	62 <when value="nofilter"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	63 </conditional>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	64 </xml>
0 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>) -->
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	66 <token name="@FORMAT@"><![CDATA[
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	67 #if $task.task_selector != 'mbr'
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	68 #if $task.msms_input.input_type_selector == "raw":
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	69 #set $format = '.raw'
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	70 #else
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	71 #set $format = '.mzml'
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	72 #end if
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	73 #else:
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	74 #set $format = '.tabular'
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	75 #end if
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	76 ]]></token>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	77 <token name="@IDENT_INPUT_ARG_MULTIPLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	78 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	79 --tsv_list
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	80 #for $value in $task.ident_input.ident_input_file:
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	81 './ident_inputs/$value.element_identifier$format'
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	82 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	83 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	84 <token name="@IDENT_INPUT_ARG_SINGLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	85 ## this is where the ident input gets passed to moff/moff_all/moff_mbr
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	86 --tsv_list './ident_inputs/${task.ident_input.ident_input_file.element_identifier}$format'
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	87 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	88 <token name="@WRANGLE_IDENT_INPUT_SINGLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	89 mkdir ./ident_inputs &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	90 #if $task.ident_input.input_type_selector == "ps":
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	91 cp '$task.ident_input.ident_input_file' './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	92 #else
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	93 cp '$task.ident_input.ident_input_file' ./tempfile1.tab &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	94 ## optionally remove first line
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	95 #if $task.ident_input.remove_header:
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	96 sed -i '1d' ./tempfile1.tab &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	97 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	98 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	99 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > ./tempfile2.tab &&
132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	100 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" ./tempfile1.tab >> ./tempfile2.tab &&
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	101 mv ./tempfile2.tab './ident_inputs/$task.ident_input.ident_input_file.element_identifier$format' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	102 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	103 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	104 <token name="@WRANGLE_IDENT_INPUT_MULTIPLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	105 mkdir ./ident_inputs &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	106 #if $task.ident_input.input_type_selector == "ps":
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	107 #for $value in $task.ident_input.ident_input_file:
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	108 cp '${value}' './ident_inputs/${value.element_identifier}$format' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	109 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	110 #else
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	111 #for $i, $value in enumerate($task.ident_input.ident_input_file):
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	112 cp '${value}' './tempfile${i}_1.tab' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	113 ## optionally remove first line
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	114 #if $task.ident_input.remove_header:
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	115 sed -i '1d' './tempfile${i}_1.tab' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	116 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	117 ## header row with correct names: "peptide", "prot", "mod_peptide", "rt", "mz", "mass", and "charge"
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	118 echo -e "peptide\tprot\tmod_peptide\trt\tmz\tmass\tcharge" > './tempfile${i}_2.tab' &&
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	119 awk 'BEGIN{OFS="\t"; FS="\t"}{print \$pep,\$prot,\$mod,\$rt,\$mz,\$mass,\$charge}' pep="${task.ident_input.peptide}" prot="$task.ident_input.prot" mod="$task.ident_input.mod_peptide" rt="$task.ident_input.rt" mz="$task.ident_input.mz" mass="$task.ident_input.mass" charge="$task.ident_input.charge" './tempfile${i}_1.tab' >> './tempfile${i}_2.tab' &&
b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	120 mv './tempfile${i}_2.tab' './ident_inputs/${value.element_identifier}$format' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	121 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	122 #end if
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	123 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	124 <token name="@RAW_INPUT_ARG_SINGLE@"><![CDATA[
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	125 --raw_list './raws/$task.msms_input.raw_list.element_identifier$format'
0 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="@RAW_INPUT_ARG_MULTIPLE@"><![CDATA[
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	128 --raw_list
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	129 #for $value in $task.msms_input.raw_list:
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	130 './raws/$value.element_identifier$format'
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	131 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	132 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	133 <token name="@WRANGLE_RAW_INPUT_SINGLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	134 mkdir ./raws &&
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	135 ## for files, need to softlink the name to the history item
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	136 ln -s '$task.msms_input.raw_list' './raws/$task.msms_input.raw_list.element_identifier$format' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	137 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	138 <token name="@WRANGLE_RAW_INPUT_MULTIPLE@"><![CDATA[
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	139 mkdir ./raws &&
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	140 ## for files, need to softlink the name to the history item
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	141 #for $value in $task.msms_input.raw_list:
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	142 ln -s '$value' './raws/$value.element_identifier$format' &&
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	143 #end for
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	144 ]]></token>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	145 </macros>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	146 <requirements>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	147 <requirement type="package" version="@VERSION@">moff</requirement>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	148 </requirements>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	149 <version_command>echo @VERSION@</version_command>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	150 <command detect_errors="aggressive"><![CDATA[
3 b7512ccf24f6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit c593ff2b871b95505064ee87dff7792165d67d97 galaxyp parents: 2 diff changeset	151 @FORMAT@
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	152 mkdir ./out &&
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	153 #if $task.task_selector == "moff":
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	154 @WRANGLE_IDENT_INPUT_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	155 @WRANGLE_RAW_INPUT_SINGLE@
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	156 moff_all.py
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	157 @IDENT_INPUT_ARG_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	158 @RAW_INPUT_ARG_SINGLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	159 --tol $task.tol
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	160 --mbr $task.mbr
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	161 --xic_length $task.xic_length
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	162 --rt_peak_win $task.rt_peak_win
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	163 --rt_peak_win_match $task.rt_peak_win_match
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	164 --loc_out ./out
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	165 #if str( $task.match_filter.filter_flags ) == "filter":
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	166 --match_filter
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	167 --sample_size $task.match_filter.sample_size
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	168 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	169 #if ($task.match_filter.ptm_file):
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	170 --ptm_file '$task.match_filter.ptm_file'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	171 #else:
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	172 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	173 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	174 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	175 #if ($task.peptide_summary):
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	176 --peptide_summary
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	177 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	178 #if $task.peptide_summary:
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	179 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	180 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	181 &&
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	182 mv ./out/*moff_result.txt '$output_table'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	183 &&
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	184 mv ./out/*.log '$output_logs'
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	185 #else if $task.task_selector == "mbr":
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	186 @WRANGLE_IDENT_INPUT_MULTIPLE@
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	187 moff_all.py
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	188 @IDENT_INPUT_ARG_MULTIPLE@
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	189 --mbr $task.mbr
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	190 --raw_list
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	191 &&
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	192 mv ./mbr_output/* ./out
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	193 #else:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	194 ## moff_all (mbr followed by apex)
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	195 @WRANGLE_IDENT_INPUT_SINGLE@
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	196 @WRANGLE_RAW_INPUT_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	197 moff_all.py
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	198 @IDENT_INPUT_ARG_SINGLE@
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	199 @RAW_INPUT_ARG_MULTIPLE@
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	200 --tol $task.tol
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	201 --mbr $task.mbr
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	202 --xic_length $task.xic_length
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	203 --rt_peak_win $task.rt_peak_win
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	204 --rt_peak_win_match $task.rt_peak_win_match
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	205 --loc_out ./out
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	206 #if ($task.peptide_summary):
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	207 --peptide_summary
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	208 #end if
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	209 #if str( $task.match_filter.filter_flags ) == "filter":
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	210 --match_filter
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	211 --sample_size $task.match_filter.sample_size
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	212 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	213 #if ($task.match_filter.ptm_file):
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	214 --ptm_file '$task.match_filter.ptm_file'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	215 #else:
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	216 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	217 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	218 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	219
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	220 #if $task.peptide_summary:
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	221 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	222 #end if
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	223 #end if
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	224 ]]></command>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	225 <inputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	226 <conditional name="task">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	227 <param name="task_selector" type="select" label="Choose which module to run">
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	228 <option value="moff">Apex intensity</option>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	229 <option value="mbr">Match between runs</option>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	230 <option value="all">All (match-between-runs followed by quantitation)</option>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	231 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	232 <when value = "moff">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	233 <expand macro="ident_input_macro" allow_multiple="false"/>
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	234 <conditional name="msms_input">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	235 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	236 <option value="raw">Thermo RAW file</option>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	237 <option value="mzml">mzML</option>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	238 </param>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	239 <when value="raw">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	240 <param argument="--raw_list" type="data" multiple="false" format="thermo.raw" label="RAW file(s)"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	241 </when>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	242 <when value="mzml">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	243 <param argument="--raw_list" type="data" multiple="false" format="mzml" label="mzML file(s)"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	244 </when>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	245 </conditional>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	246
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	247
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	248 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	249 help="Specify the tolerance parameter in ppm." />
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	250 <param argument="--mbr" type="text" value="off" label="moFF workflow"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	251 help="select the moFF workflow" />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	252 <param argument="--xic_length" type="float" value="3.0" label="retention time windows for XiC"
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	253 help="Specify rt window for xic in minutes." />
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	254 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	255 help="Specify rt window for the peak in minutes." />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	256 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	257 help="Specify the retention time window for the matched peak in minutes." />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	258 <expand macro="filt_matched_peptide"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	259 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	260 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	261 <when value="mbr">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	262 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	263 <param argument="--mbr" type="text" value="only" label="moFF workflow"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	264 help="select the moFF workflow" />
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	265 </when>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	266 <when value="all">
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	267 <expand macro="ident_input_macro" allow_multiple="false" input_type="data"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	268 <conditional name="msms_input">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	269 <param name="input_type_selector" type="select" label="Choose the format for the MS/MS file">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	270 <option value="raw">Thermo RAW file</option>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	271 <option value="mzml">mzML</option>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	272 </param>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	273 <when value="raw">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	274 <param argument="--raw_list" type="data" multiple="true" min="2" format="thermo.raw" label="RAW file(s)"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	275 </when>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	276 <when value="mzml">
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	277 <param argument="--raw_list" type="data" multiple="true" min="2" format="mzml" label="mzML file(s)"/>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	278 </when>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	279 </conditional>
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	280
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	281 <param argument="--tol" type="float" value="10" label="Tolerance parameter"
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	282 help="Specify the tolerance parameter in ppm." />
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	283 <param argument="--mbr" type="text" value="on" label="moFF workflow"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	284 help="select the moFF workflow" />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	285 <param argument="--xic_length" type="float" value="3.0" label="retention time windows for XiC"
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	286 help="Specify rt window for xic in minutes." />
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	287 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	288 help="Specify the retention time window for the peak in minutes." />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	289 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	290 help="Specify the retention time window for the matched peak in minutes." />
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	291 <expand macro="filt_matched_peptide"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	292 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	293 </when>
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	294 </conditional>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	295 </inputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	296 <outputs>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	297 <data format="tabular" name="output_table" label="${tool.name} on ${on_string}: quantification">
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	298 <filter>task['task_selector']=='moff'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	299 </data>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	300 <data format="txt" name="output_logs" label="${tool.name} ${on_string}: log">
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	301 <filter>task['task_selector']=='moff'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	302 </data>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	303 <collection name="ident_output" type="list" label="${tool.name} on ${on_string}: quantification">
132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	304 <filter>task['task_selector']=='all'</filter>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	305 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	306 </collection>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	307 <collection name="ident_output_mbr" type="list" label="${tool.name} on ${on_string}: matched">
132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	308 <filter>task['task_selector']=='mbr'</filter>
132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	309 <discover_datasets pattern="(?P<designation>.*)\.txt" directory="out" format="tabular"/>
132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	310 </collection>
132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	311 <collection name="log_output" type="list" label="${tool.name} on ${on_string}: logs">
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	312 <filter>task['task_selector']=='all' or task['task_selector']=='mbr'</filter>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	313 <discover_datasets pattern="(?P<designation>.*)\.log" directory="out" format="txt"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	314 </collection>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	315 <data format="tabular" name="output_peptide_summary" label="${tool.name} on ${on_string}: peptide summary">
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	316 <filter>(task['task_selector']=='all' or task['task_selector']=='moff') and task['peptide_summary'] </filter>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	317 </data>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	318 </outputs>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	319 <tests>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	320 <!-- test mbr -->
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	321 <test>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	322 <param name="task\|task_selector" value="mbr"/>
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	323 <param name="ident_input\|input_type_selector" value="ps"/>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	324 <param name="ident_input_file">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	325 <collection type="list">
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	326 <element name="mbr_test1" value="input/mbr_test1.tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	327 <element name="mbr_test2" value="input/mbr_test2.tabular"/>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	328 </collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	329 </param>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	330 <param name="ext" value="tabular"/>
2 132122c34950 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit ba04453c8ce4bd23a138e3e546ad17064b3ac38c galaxyp parents: 1 diff changeset	331 <output_collection name="ident_output_mbr" type="list" count="2">
1 5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	332 <element name="mbr_test1_match">
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	333 <assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	334 <has_text text="NH2-QVEEAVQSDDK-COOH"/>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	335 <has_text text="NH2-RDVGINNTVK-COOH"/>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	336 </assert_contents>
5e5c91fab75c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit cfc15ad41da358a04be60d50c7540ac7d75e1b41 galaxyp parents: 0 diff changeset	337 </element>
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	338 </output_collection>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	339 </test>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	340 </tests>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	341 <help>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	342 <![CDATA[
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	343
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	344 Description
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	345
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	346 moFF (a Modest Feature Finder) is an OS independent tool designed to extract
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	347 apex MS1 intensity using a set of identified MS2 peptides.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	348 It currently uses a Go library to directly extract data from Thermo Raw spectrum files,
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	349 eliminating the need for conversions from other formats.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	350 Moreover, moFF also allows one to work directly with mzML files.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	351
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	352 Usage
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	353
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	354 Modules:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	355
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	356 1. Apex Intensity: this is used for a single pair of files, one identification and one spectrum file.
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	357 2. Match between runs (MBR): for multiple identification files, share MS2 identified peptides between runs and predict the retention time.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	358 3. All (match between runs followed by apex intensity): this is used for more than one pair of identification and spectrum files.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	359
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	360 If both match between runs and apex intensity are desired, it is best to run them both at once (i.e., run the 'All' module).
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	361 The MBR module is mainly useful for observing the intermediate steps of the algorithm - its outputs are not able to be used as inputs in moFF or in other tools.
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	362 If quantification of multiple files without MBR is desired, the apex intensity module may be run with multiple files or a dataset collection in batch mode.
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	363 In either case, moFF must be given the paired files at the same time - thus the best method is to construct a dataset collection in which the raw and identification files are in the same order.
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	364
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	365 Inputs:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	366
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	367 - Identification file: this can either be a generic tabular file or the standard PSM report from PeptideShaker.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	368 If it is a generic tabular file, please select the columns corresponding to the required information.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	369 - MS/MS file: this can either be a Thermo raw file or an mzML file.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	370
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	371 A given pair of files must have the exact same display name, not including the extension;
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	372 e.g. ``example1.tabular`` and ``example1.mzml``.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	373 If the display names are different, simply change them in the history menu.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	374 For multiple files (the MBR or All modules), the identification and spectrum files must be provided as dataset collections.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	375 This allows for usage of the output dataset collections in workflows.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	376
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	377 Parameters:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	378
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	379 All the parameters related to the the time windows (``rt_w``, ``rt_p``, ``rt_p_match``) are basically the
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	380 half of the entire time windows where the apex peak is searched or the XIC is retrieved.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	381 For correct rt windows, we suggest you set the ``rt_p`` value equal to or slighly greater than the
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	382 dynamic exclusion duration set in your machine. We suggest also to set the
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	383 ``rt_p_match`` always slightly bigger than tha values used for ``rt_p``.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	384 Outputs:
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	385 When used in the single file mode ("Apex intensity" module), the outputs are 2 (or 3) files: a log file, a quantitation file,
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	386 and (optionally) a peptide summary, with intensities aggregated across peptides. When used in the multiple file mode ("All"),
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	387 the outputs are a dataset collection of log files (one per identification file), a dataset collection of quantification files, and (optionally) a peptide summary.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	388 If used with a generic tabular format, the only columns in the output file are the 7 columns selected while using moFF plus the columns that moFF adds. Other columns are discarded.
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	389
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	390 More Information
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	391
4 20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	392 See the moFF Github site at https://github.com/compomics/moFF,
20ded57bc56b "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52" galaxyp parents: 3 diff changeset	393 and the publication at https://dx.doi.org/10.1038/nmeth.4075
0 28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	394 ]]>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	395 </help>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	396 <citations>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	397 <citation type="doi">10.1038/nmeth.4075</citation>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	398 </citations>
28c4a4a8bbd3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit bc0fad49e3ba73fa5b5b326e940adf9e11854d94 galaxyp parents: diff changeset	399 </tool>

Mercurial > repos > galaxyp > proteomics_moff

annotate moff.xml @ 4:20ded57bc56b draft default tip