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comparison lcms-interval-scheduling.xml @ 0:21a76537a900 draft

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
author tomnl
date Tue, 27 Mar 2018 06:53:12 -0400
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1 <tool id="lcms_interval_scheduling" name="lcms_interval_scheduling" version="0.0.2">
2 <requirements>
3 <requirement type="package" >r</requirement>
4 <requirement type="package" >r-optparse</requirement>
5 <requirement type="package" >r-xcmswrapper</requirement>
6 </requirements>
7 <description>Generate target lists from LC-MS features for a fragmentation experiment
8 </description>
9
10 <stdio>
11 <exit_code range="1:" />
12 </stdio>
13 <command interpreter="Rscript"><![CDATA[
14 lcms-interval-scheduling.R
15
16 --sample_peaklist=$sample_peaklist
17 --blank_peaklist=$blank_peaklist
18 --topn=$topn
19 --out_dir=.
20 --method=$method_select.method
21 #if $method_select.method=='metshot'
22 #if $method_select.fillgaps
23 --fillgaps
24 #end if
25 #elif $method_select.method=='simple'
26 --maxms2=$method_select.maxms2
27 --ilimit=$method_select.ilimit
28 #else
29 --overlappingP=$method_select.overlappingP
30 #end if
31 --widthFactor=$widthFactor
32 --minWidth=$minWidth
33 --shift=$shift
34 --samplelistNm=$samplelistNm
35 #if $fullpw
36 --fullpw
37 #end if
38 --b_widthFactor=$b_widthFactor
39 --b_shift=$b_shift
40 --b_exclu_limit=$b_exclu_limit
41 --b_minWidth=$b_minWidth
42 --polarity=$polarity
43 #if $dma_nearline_cond.dma=='yes'
44 --blankClass=$dma_nearline_cond.blankClass
45 --filterS=$dma_nearline_cond.filterS
46 --dmaNearline
47 #end if
48 --intensityCN=$intensityCN
49 --sortCN=$sortCN
50 ]]></command>
51 <inputs>
52 <param type="data" name="sample_peaklist" label="Sample peaklist" format="tsv,tabular"
53 help="The peaklist from the samples to be scheduled for fragmentation"/>
54
55 <param type="data" name="blank_peaklist" label="Blank peaklist" format="tsv,tabular"
56 help="The peaklist of blank features to avoid when performing fragmentation"/>
57
58 <param type="data" name="topn" label="Topn blank peaklist" format="tsv,tabular"
59 help="The top (n) blank peaks determined from windows of the spectrum (i.e. not using XCMS)"/>
60
61 <conditional name="method_select">
62 <param name="method" type="select" label="Nearline method">
63 <option value="simple" >Simple nearline (divide equally amongst runs) </option>
64 <option value="interval">Interval schedule with defined overlap</option>
65 <option value="interval_min_overlap" selected="true">Interval schedule with defined overlap. Overlap is also minimized</option>
66 <option value="metshot">Original metshot algorithm (No overlapping features)</option>
67 </param>
68 <when value="metshot">
69 <param name="fillGaps" type="boolean" label="Fill gaps"/>
70 </when>
71 <when value="simple">
72 <param name="maxms2" type="integer" label="Max MS2 per run" value="2000"/>
73 <param name="ilimit" type="float" label="Intensity (peak area) limit to be included" value="5000"/>
74 </when>
75 <when value="interval">
76 <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/>
77 </when>
78 <when value="interval_min_overlap">
79 <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/>
80 </when>
81 </conditional>
82
83 <param name="widthFactor" type="float" label="Width factor" value="1"
84 help="Increase the width of the peaks by the chosen factor "/>
85
86 <param name="minWidth" type="float" label="Minimum width of peak (sec)" value="5"
87 help="The time range will always be >= to this value (even if the prior peak width is calculated
88 to be smaller)"/>
89
90 <param name="shift" type="float" label="Shift (sec)" value="0" help="Shift all the peaks by value to account for drift"/>
91 <param name="samplelistNm" type="integer" label="Number of MS2 runs to perform" value="4"/>
92 <param name="fullpw" type="boolean" label="Use full peak width?" help="" />
93 <param name="b_widthFactor" type="float" label="Width factor (for blank)" value="2"
94 help="Increase the width of the peaks by the chosen factor "/>
95
96 <param name="b_minWidth" type="float" label="Minimum width of peak (sec) (for blank)" value="5"
97 help="The time range will always be >= to this value (even if the prior peak width is calculated
98 to be smaller) (for blank)"/>
99
100
101 <param name="b_shift" type="float" label="Shift (for blank) (sec)" value="0" help="Shift all the peaks by value to account for drift"/>
102 <param name="b_exclu_limit" type="integer" label="Exclusion limit" value="5000" help="Limit of peaks to put on exclusion limit"/>
103 <param name="polarity" type="select" label="Polarity">
104 <option value="positive" selected="true" >Positive</option>
105 <option value="negative" >Negative</option>
106 </param>
107
108 <param name="sortCN" type="text" label="column of sample peaklist to order by" value="totalS"
109 help="default value corresponds if the tool 'deconrank' has been run prior. The 'total score'
110 column is based on multiple criteria (see deconrank tool).
111 If not using the deconrank tool, any other column can be used e.g. intensity (peak area)"/>
112
113 <param name="intensityCN" type="text" label="column to use for intensity (peak area) for sample" value="i"/>
114
115
116 <conditional name="dma_nearline_cond">
117 <param name="dma" type="select" label="Use as part of DMA nearline workflow?"
118 help="If using within the nearline LC-MS workflow then certain processing needs to be performed,
119 including filtering out peaks that are not to be scheduled">
120 <option value="yes">Yes</option>
121 <option value="no" select="no">No</option>
122 </param>
123 <when value="yes">
124 <param name="blankClass" type="text" label="Blank class" value="blank"
125 help="Note that this will have to change if the blank class has a different name. Uses the valid
126 column e.g. [blank_name]_valid.
127 If he value is 1 (we keep) if 0 (we do not use)" />
128 <param name="filterS" type="text" label="Column name to filter sample on" value="excludedFinal"
129 help="This is a bit confusing.. But if this value is 1 then (we exclude) and if 0 (we keep for the
130 sample)"/>
131 </when>
132 </conditional>
133
134 </inputs>
135 <outputs>
136 <collection name="inclusion_lists" type="list" label="${tool.name} on ${on_string}: inclusion lists">
137 <discover_datasets pattern="(?P&lt;designation&gt;.+inclusion.+).csv" format="csv" directory="." />
138 </collection>
139 <collection name="exclusion_lists" type="list" label="${tool.name} on ${on_string}: exclusion lists">
140 <discover_datasets pattern="(?P&lt;designation&gt;.+exclusion.+).csv" format="csv" directory="." />
141 </collection>
142 <data format="pdf" name="overlap_plots_positive" label="${tool.name} on ${on_string}: overlap plots"
143 from_work_dir="overlap_plots_positive.pdf"/>
144
145 </outputs>
146 <tests>
147 </tests>
148 <help><![CDATA[
149
150 ]]></help>
151 </tool>