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comparison isoread.xml @ 0:63ae92b7f425 draft

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author glogobyte
date Wed, 13 Oct 2021 16:03:19 +0000
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1
2 <tool id="IsoRead" name="IsoRead: miR and isomiR identification and classification" version="0.1.0">
3 <requirements>
4 <requirement type="package" version="1.7">fpdf</requirement>
5 <requirement type="package" version="0.8">logomaker</requirement>
6 <requirement type="package" version="0.6.0">plotnine</requirement>
7 <requirement type="package" version="3.7.4">python</requirement>
8 <requirement type="package" version="1.17.3">numpy</requirement>
9 <requirement type="package" version="3.1.2">matplotlib</requirement>
10 <requirement type="package" version="0.9.0">seaborn</requirement>
11 <requirement type="package" version="1.0.3">pandas</requirement>
12 </requirements>
13 <command>
14 #set controls=[]
15 #for $input in $control#
16 $controls.extend([str($input.element_identifier),str($input)])
17 #end for#
18 #set treateds=[]
19 #for $input in $treated#
20 $treateds.extend([str($input.element_identifier),str($input)])
21 #end for#
22 #if $mir_input.database == "1":
23 #if $f.fil == "1":
24 #set path=$mir_input.genome1.fields.path
25 python -W ignore $__tool_directory__/mirbase.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2"
26 #end if
27 #if $f.fil == "2":
28 #set path=$mir_input.genome1.fields.path
29 python -W ignore $__tool_directory__/mirbase.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "$f.fil1" -counts "$f.fil2" -name1 "$fal1" -name2 "$fal2"
30 #end if
31 #else:
32 #if $f.fil == "1":
33 #set path=$mir_input.genome2.fields.value
34 python -W ignore $__tool_directory__/mirgene.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2"
35 #end if
36 #if $f.fil == "2":
37 #set path=$mir_input.genome2.fields.value
38 python -W ignore $__tool_directory__/mirgene.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -percentage "$f.fil1" -counts "$f.fil2" -name1 "$fal1" -name2 "$fal2"
39 #end if
40 #end if
41
42 </command>
43 <inputs>
44 <param name="analysis" type="select" label="Discover miR with templated or/and non-templated isomiRs" help="Choose the category of miRNAs for detection">
45 <option value="1" selected="true">Detection of only templated miRNAs</option>
46 <option value="2">Detection of templated and non-templated miRNAs</option>
47 </param>
48 <conditional name="mir_input">
49 <param name="database" type="select" label="Reference miRNA DB" help="Choose which database prefer to be used.">
50 <option value="1" selected="true">MirBase</option>
51 <option value="2">MirGene</option>
52 </param>
53 <when value="1">
54 <param name="genome1" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest are not listed, contact the Galaxy team">
55 <options from_data_table="mirbase" />
56 </param>
57 </when>
58 <when value="2">
59 <param name="genome2" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest are not listed, contact the Galaxy team">
60 <options from_data_table="mirgene" />
61 </param>
62 </when>
63 </conditional>
64 <param name="fal1" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/>
65 <param name="control" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" />
66 <param name="fal2" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/>
67 <param name="treated" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" />
68 <conditional name="f">
69 <param name="fil" type="select" label="Filter low counts" help="Treat genes with very low expression as unexpressed and filter out">
70 <option value="1" selected="true">No</option>
71 <option value="2">Yes</option>
72 </param>
73 <when value="2">
74 <param name="fil1" type="integer" value="0" label="Minimum percentage of the samples" help="Filter out all genes that do not meet the Minimum counts in at least this many samples of every category"/>
75 <param name="fil2" type="integer" value="0" label="Minimum counts" help="Filter out all genes that do not meet this minimum count"/>
76 </when>
77 <when value="1">
78 </when>
79 </conditional>
80 <param name="db" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Database files" />
81 <param name="cmatrix" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Output Matrix files, one for each factor level" />
82 <param name="c_files" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Count tables, one for each sample" />
83 </inputs>
84 <outputs>
85 <collection name="list_output1" type="list" label="Database ${fal1} templated" >
86 <discover_datasets pattern="__name__" format="tabular" directory="split1" />
87 <filter>db == 1 and (analysis == "1" or analysis == "2")</filter>
88 </collection>
89 <collection name="list_output2" type="list" label="Database ${fal2} templated" >
90 <discover_datasets pattern="__name__" format="tabular" directory="split2" />
91 <filter>db == 1 and (analysis == "1" or analysis == "2")</filter>
92 </collection>
93 <collection name="list_output3" type="list" label="Database ${fal1} non-templated" >
94 <discover_datasets pattern="__name__" format="tabular" directory="split3" />
95 <filter>db == 1 and analysis == "2"</filter>
96 </collection>
97 <collection name="list_output4" type="list" label="Database ${fal2} non-templated" >
98 <discover_datasets pattern="__name__" format="tabular" directory="split4" />
99 <filter>db == 1 and analysis == "2"</filter>
100 </collection>
101
102 <collection name="Counts" type="list" label="Count Matrices" >
103 <discover_datasets pattern="__name__" format="tabular" directory="Counts" />
104 <filter>cmatrix==1</filter>
105 </collection>
106 <collection name="list_output9" type="list" label="Count files ${fal1} for Differential Expression" >
107 <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_con" />
108 <filter>c_files==1 and (analysis == "1")</filter>
109 </collection>
110 <collection name="list_output10" type="list" label="Count files ${fal2} for Differential Expression" >
111 <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_tre" />
112 <filter>c_files==1 and (analysis == "1")</filter>
113 </collection>
114 <collection name="list_output11" type="list" label="Count files ${fal1} for Differential Expression" >
115 <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_con" />
116 <filter>c_files==1 and analysis == "2"</filter>
117 </collection>
118 <collection name="list_output12" type="list" label="Count files ${fal2} for Differential Expression" >
119 <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_tre" />
120 <filter>c_files==1 and analysis == "2"</filter>
121 </collection>
122
123 <data name="Results non templated treated1" format="pdf" label="IsomiR Profile Report" from_work_dir="$__tool_directory__/report1.pdf" />
124 </outputs>
125 <help>
126 </help>
127 </tool>