ms_to_peakforest_it: ms2pf

annotate ms2pf_it.xml @ 1:7e3085fc60c1 draft default tip

master branch Updating

author	lain
date	Wed, 30 Aug 2023 14:21:18 +0000
parents	b58b229c4cbf
children

rev	line source
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	1 <tool id="ms_to_peakforest_it" name="MS To PeakForest IT" tool_type="interactive" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	2 <description>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	3 adds you MS spectrum to peakforest.
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	4 </description>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	5 <macros>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	6 <token name="@TOOL_VERSION@">1.2.1</token>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	7 <token name="@VERSION_SUFFIX@">0</token>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	8 </macros>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	9 <requirements>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	10 <container type="docker">quay.io/pfem/ms2peakforest:@TOOL_VERSION@</container>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	11 </requirements>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	12 <entry_points>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	13 <entry_point name="MS to PeakForest, with ${','.join(str(i.name) for i in $input)}" requires_domain="True">
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	14 <port>8000</port>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	15 <url>/</url>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	16 </entry_point>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	17 </entry_points>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	18 <version_command>
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	19 <![CDATA[
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	20 python3 '$__tool_directory__/server.py' --version \| head -n 1
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	21 ]]>
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	22 </version_command>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	23 <command><![CDATA[
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	24 cd /ms2pf
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	25 && python3 '$__tool_directory__/server.py'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	26 --input '${','.join(map(str, $input))}'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	27 --raw-metadata '${advanced.raw_metadata_sep.join(str(i.name) for i in $input)}'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	28 --raw-metadata-sep '$advanced.raw_metadata_sep'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	29 --method '$method'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	30 --peakforest-url '$peakforest_url'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	31 --peakforest-token '$peakforest_token'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	32 --spectrum-type '$spectrum_type'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	33 --sample-type '$sample_type'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	34 --sample-type '$sample_type'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	35 #if $advanced.rt_min != 0.0 and $advanced.rt_max != 0.0
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	36 --rt-min '$advanced.rt_min'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	37 --rt-max '$advanced.rt_max'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	38 #else
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	39 --rt-min ''
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	40 --rt-max ''
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	41 #end if
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	42 --polarity '$polarity'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	43 --name '$advanced.name'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	44 #if $advanced.do_output_json:
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	45 --output-json '$json_output'
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	46 #end if
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	47 $advanced.verbose
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	48 $advanced.debug
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	49 ]]>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	50 </command>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	51 <inputs>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	52 <param argument="--input" type="data" multiple="true" format="tabular,csv,tsv"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	53 label="list of files to process"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	54 help="A data collection from fragnot or a single file from ms2snoop."
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	55 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	56 <param argument="--peakforest-url" type="select"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	57 label="PeakForest instance"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	58 help="Determines on which pf instance we push data"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	59 refresh_on_change="true"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	60 >
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	61 <option value="https://alpha.peakforest.org">alpha</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	62 <option value="https://nightly.peakforest.org">nightly</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	63 <option value="https://metabohub.peakforest.org">metabohub</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	64 </param>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	65 <param argument="--peakforest-token" type="text"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	66 label="PeakForest token"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	67 help="Please provide you api token for this instance"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	68 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	69 <param argument="--spectrum-type" type="select"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	70 label="Spectrum Type"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	71 help="Spectrum Type"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	72 refresh_on_change="true"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	73 >
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	74 <option value="LC_MS">LC-MS</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	75 <option value="LC_MSMS">LC-MSMS</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	76 <option value="GC_MS">GC-MS</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	77 </param>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	78
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	79 <param argument="--method" type="select"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	80 label="Chromatography Method"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	81 dynamic_options="[list(x.values())+[False] for x in __import__('json').loads(__import__('urllib').request.urlopen(peakforest_url+'/webapp/resources/json/list-'+ ('lc' if spectrum_type == 'LC_MS' else 'lc-msms') +'-methods.json?token='+peakforest_token).read())['methods']]"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	82 >
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	83 </param>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	84
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	85 <param argument="--sample-type" type="select"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	86 label="Sample Type"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	87 help="Sample Type"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	88 >
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	89 <option value="compound-ref">Compound Ref</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	90 <option value="compound-mix">Compound Mix</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	91 </param>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	92 <param argument="--polarity" type="select"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	93 label="polarity"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	94 help="polarity"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	95 >
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	96 <option value="positive">positive</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	97 <option value="negative">negative</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	98 <option value="neutral">neutral</option>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	99 </param>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	100 <section name="advanced">
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	101 <param argument="--name" type="text"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	102 label="name"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	103 help="name, or names separated by commas"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	104 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	105 <param argument="--rt-min" type="float" value="0.0"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	106 label="Min RT"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	107 help="The default min RT to set"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	108 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	109 <param argument="--rt-max" type="float" value="0.0"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	110 label="Max RT"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	111 help="The default max RT to set"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	112 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	113 <param argument="--raw-metadata-sep" type="text" value="XXX"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	114 label="Files names separator"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	115 help="Select a/some character·s that are not in any file name."
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	116 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	117 <param name="do_output_json" type="boolean"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	118 label="Produce JSON"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	119 help="
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	120 Select this option to output a json file of the
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	121 resulting processing.
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	122 "
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	123 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	124 <param argument="--debug" type="boolean" truevalue="--debug" falsevalue=""
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	125 label="Activate debug logs"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	126 help="Select to produce more detailed logs."
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	127 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	128 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue=""
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	129 label="Activate verbose logs"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	130 help="Select to produce more logs."
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	131 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	132 </section>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	133 </inputs>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	134 <outputs>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	135 <data name="ms2pfout" format="txt"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	136 label="${tool.name} on ${','.join(i.name for i in $input)}"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	137 />
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	138 <data name="json_output" format="json"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	139 label="JSON ${tool.name} on ${','.join(i.name for i in $input)}.json"
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	140 >
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	141 <filter>do_output_json</filter>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	142 </data>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	143 </outputs>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	144 <tests>
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	145 </tests>
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	146 <help>
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	147 <![CDATA[
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	148 .. class:: infomark
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	149
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	150 Authors Lain Pavot (lain.pavot@inrae.fr)
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	151
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	152 .. class:: infomark
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	153
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	154 ---------------------------------------------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	155
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	156 ==============
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	157 MS2 validation
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	158 ==============
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	159
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	160 -----------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	161 Description
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	162 -----------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	163
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	164
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	165 -----------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	166 Workflow position
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	167 -----------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	168
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	169 --------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	170 Upstream tools
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	171 --------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	172
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	173 +-------------------------+-----------------+--------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	174 \| Name \| output file \| format \| parameter \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	175 +=========================+=================+========+============+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	176 \| ms2snoop \| tsv \| TSV \| NA \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	177 +-------------------------+-----------------+--------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	178 \| abinitfragnot \| tsv \| TSV \| NA \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	179 +-------------------------+-----------------+--------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	180
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	181 ----------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	182 Downstream tools
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	183 ----------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	184
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	185 +-------------------------+-----------------+--------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	186 \| Name \| output file \| format \| parameter \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	187 +=========================+=================+========+============+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	188 \| NA \| NA \| NA \| NA \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	189 +-------------------------+-----------------+--------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	190
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	191
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	192 -----------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	193 Input files
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	194 -----------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	195
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	196 +----------------------------------------------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	197 \| Parameter : num + label \| Format \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	198 +===========================+==================+============+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	199 \| Output from ms2snoop or fragnot \| TSV,CSV \|
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	200 +----------------------------------------------+------------+
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	201
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	202 ----------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	203 Parameters
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	204 ----------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	205
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	206 input
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	207 \| The file to process. Should contain spectra with mz, intensities and
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	208 annotations
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	209
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	210 method
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	211 \| The method parameter tells which method was used. The value will
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	212 be the default value in the peakforest form.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	213
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	214 peakforest-url
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	215 \| The peakforest-url parameter tells which instance of peakforest to
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	216 interact with
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	217
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	218 scan_type
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	219 \| The scan_type parameter which kind of scan was used. The value will
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	220 be the default value in the peakforest form.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	221
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	222 polarity
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	223 \| The polarity parameter which polarity was used. The value will
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	224 be the default value in the peakforest form.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	225
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	226 name
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	227 \| The name parameter provides names each spectra.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	228
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	229
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	230 ------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	231 Output files
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	232 ------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	233
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	234 There is not output file. When you run this tool, keep waiting until the
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	235 « click here to display » link appears.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	236
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	237 Click on the link to display peakforest form.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	238
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	239 --------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	240 Changelog/News
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	241 --------------
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	242
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	243 1.2.0
7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	244 \| Version from images hosted on quay.io.
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	245 1.0.0
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	246 \| First version, published on the toolshed.
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	247
b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	248 ]]>
1 7e3085fc60c1 master branch Updating lain parents: 0 diff changeset	249 </help>
0 b58b229c4cbf planemo upload commit 523a9c8df173302ad38e9f15e7d82eab01736551-dirty lain parents: diff changeset	250 </tool>

Mercurial > repos > lain > ms_to_peakforest_it

annotate ms2pf_it.xml @ 1:7e3085fc60c1 draft default tip