|
6
|
1
|
|
|
2 <tool id="fa_gc_content_1" name="IsoRead: miR and isomiR identification and classification" version="0.1.0">
|
|
|
3 <description>for each sequence in a file</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="1.7">fpdf</requirement>
|
|
|
6 <requirement type="package" version="0.8">logomaker</requirement>
|
|
|
7 <requirement type="package" version="0.6.0">plotnine</requirement>
|
|
|
8 <requirement type="package" version="3.7.4">python</requirement>
|
|
|
9 <requirement type="package" version="1.17.3">numpy</requirement>
|
|
|
10 <requirement type="package" version="3.1.2">matplotlib</requirement>
|
|
|
11 <requirement type="package" version="0.9.0">seaborn</requirement>
|
|
|
12 <requirement type="package" version="1.0.3">pandas</requirement>
|
|
|
13 </requirements>
|
|
|
14 <command>
|
|
|
15 #set controls=[]
|
|
|
16 #for $input in $control#
|
|
|
17 $controls.extend([str($input.element_identifier),str($input)])
|
|
|
18 #end for#
|
|
|
19 #set treateds=[]
|
|
|
20 #for $input in $treated#
|
|
|
21 $treateds.extend([str($input.element_identifier),str($input)])
|
|
|
22 #end for#
|
|
|
23 #if $mir_input.database == "1":
|
|
|
24 #if $f.fil == "1":
|
|
|
25 #set path=$mir_input.genome1.fields.path
|
|
|
26 python -W ignore $__tool_directory__/mirbase_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2"
|
|
|
27 #end if
|
|
|
28 #if $f.fil == "2":
|
|
|
29 #set path=$mir_input.genome1.fields.path
|
|
|
30 python -W ignore $__tool_directory__/mirbase_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "$f.fil1" -counts "$f.fil2" -name1 "$fal1" -name2 "$fal2"
|
|
|
31 #end if
|
|
|
32 #else:
|
|
|
33 #if $f.fil == "1":
|
|
|
34 #set path=$mir_input.genome2.fields.value
|
|
|
35 python -W ignore $__tool_directory__/mirgene_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "-1" -counts "-1" -name1 "$fal1" -name2 "$fal2"
|
|
|
36 #end if
|
|
|
37 #if $f.fil == "2":
|
|
|
38 #set path=$mir_input.genome2.fields.value
|
|
|
39 python -W ignore $__tool_directory__/mirgene_ultra_v2.py -con $controls -tre $treateds -analysis $analysis -tool_dir $__tool_directory__ -gen "$path" -f "$mir_input.database" -umis $umis -percentage "$f.fil1" -counts "$f.fil2" -name1 "$fal1" -name2 "$fal2"
|
|
|
40 #end if
|
|
|
41 #end if
|
|
|
42
|
|
|
43 </command>
|
|
|
44 <inputs>
|
|
|
45 <param name="analysis" type="select" label="Discover miR with templated or/and non-templated isomiRs" help="Choose the category of miRNAs for detection">
|
|
|
46 <option value="1" selected="true">Detection of only templated miRNAs</option>
|
|
|
47 <option value="2">Detection of templated and non-templated miRNAs</option>
|
|
|
48 </param>
|
|
|
49
|
|
|
50 <conditional name="mir_input">
|
|
|
51 <param name="database" type="select" label="Choose Database of miRNAs organisms" help="Choose which database prefer to be used.">
|
|
|
52 <option value="1" selected="true">MirBase</option>
|
|
|
53 <option value="2">MirGene</option>
|
|
|
54 </param>
|
|
|
55 <when value="1">
|
|
|
56 <param name="genome1" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
|
|
|
57 <options from_data_table="n_spiecies" />
|
|
|
58 </param>
|
|
|
59 </when>
|
|
|
60 <when value="2">
|
|
|
61 <param name="genome2" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest is not listed, contact the Galaxy team">
|
|
|
62 <options from_data_table="mirgene" />
|
|
|
63 </param>
|
|
|
64 </when>
|
|
|
65 </conditional>
|
|
|
66
|
|
|
67
|
|
|
68 <param name="fal1" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/>
|
|
|
69 <param name="control" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" />
|
|
|
70 <param name="fal2" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/>
|
|
|
71 <param name="treated" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" />
|
|
|
72
|
|
|
73 <conditional name="f">
|
|
|
74 <param name="fil" type="select" label="Filter low counts" help="Treat genes with very low expression as unexpressed and filter out">
|
|
|
75 <option value="1" selected="true">No</option>
|
|
|
76 <option value="2">Yes</option>
|
|
|
77 </param>
|
|
|
78 <when value="2">
|
|
|
79 <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"/>
|
|
|
80 <param name="fil2" type="integer" value="0" label="Minimum counts" help="Filter out all genes that do not meet this minimum count"/>
|
|
|
81 </when>
|
|
|
82 <when value="1">
|
|
|
83 </when>
|
|
|
84 </conditional>
|
|
|
85
|
|
|
86 <param name="db" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Database files" />
|
|
|
87 <param name="cmatrix" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Output Matrix files, one for each factor level" />
|
|
|
88 <param name="c_files" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Count tables, one for each sample" />
|
|
|
89 <param name="umis" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Collapsing sam files if samples include UMIs" />
|
|
|
90 </inputs>
|
|
|
91 <outputs>
|
|
|
92 <collection name="list_output1" type="list" label="Database ${fal1} templated" >
|
|
|
93 <discover_datasets pattern="__name__" format="tabular" directory="split1" />
|
|
|
94 <filter>db == 1 and (analysis == "1" or analysis == "2")</filter>
|
|
|
95 </collection>
|
|
|
96 <collection name="list_output2" type="list" label="Database ${fal2} templated" >
|
|
|
97 <discover_datasets pattern="__name__" format="tabular" directory="split2" />
|
|
|
98 <filter>db == 1 and (analysis == "1" or analysis == "2")</filter>
|
|
|
99 </collection>
|
|
|
100 <collection name="list_output3" type="list" label="Database ${fal1} non-templated" >
|
|
|
101 <discover_datasets pattern="__name__" format="tabular" directory="split3" />
|
|
|
102 <filter>db == 1 and analysis == "2"</filter>
|
|
|
103 </collection>
|
|
|
104 <collection name="list_output4" type="list" label="Database ${fal2} non-templated" >
|
|
|
105 <discover_datasets pattern="__name__" format="tabular" directory="split4" />
|
|
|
106 <filter>db == 1 and analysis == "2"</filter>
|
|
|
107 </collection>
|
|
|
108
|
|
|
109 <collection name="Counts" type="list" label="Count Matrices" >
|
|
|
110 <discover_datasets pattern="__name__" format="tabular" directory="Counts" />
|
|
|
111 <filter>cmatrix==1</filter>
|
|
|
112 </collection>
|
|
|
113
|
|
|
114
|
|
|
115 <collection name="list_output9" type="list" label="Count files ${fal1} for Differential Expression" >
|
|
|
116 <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_con" />
|
|
|
117 <filter>c_files==1 and (analysis == "1")</filter>
|
|
|
118 </collection>
|
|
|
119 <collection name="list_output10" type="list" label="Count files ${fal2} for Differential Expression" >
|
|
|
120 <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_tre" />
|
|
|
121 <filter>c_files==1 and (analysis == "1")</filter>
|
|
|
122 </collection>
|
|
|
123 <collection name="list_output11" type="list" label="Count files ${fal1} for Differential Expression" >
|
|
|
124 <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_con" />
|
|
|
125 <filter>c_files==1 and analysis == "2"</filter>
|
|
|
126 </collection>
|
|
|
127 <collection name="list_output12" type="list" label="Count files ${fal2} for Differential Expression" >
|
|
|
128 <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_tre" />
|
|
|
129 <filter>c_files==1 and analysis == "2"</filter>
|
|
|
130 </collection>
|
|
|
131
|
|
|
132 <data name="Results non templated treated1" format="pdf" label="PDF" from_work_dir="$__tool_directory__/report1.pdf" />
|
|
|
133 </outputs>
|
|
|
134 <help>
|
|
|
135 </help>
|
|
|
136 </tool>
|
