annotate isoread.xml @ 22:958330b9bce3 draft

Uploaded
author glogobyte
date Wed, 20 Oct 2021 12:11:30 +0000
parents 63ae92b7f425
children 293aa8cbbc20
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
1
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
2 <tool id="IsoRead" name="IsoRead: miR and isomiR identification and classification" version="0.1.0">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
3 <requirements>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
4 <requirement type="package" version="1.7">fpdf</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
5 <requirement type="package" version="0.8">logomaker</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
6 <requirement type="package" version="0.6.0">plotnine</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
7 <requirement type="package" version="3.7.4">python</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
8 <requirement type="package" version="1.17.3">numpy</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
9 <requirement type="package" version="3.1.2">matplotlib</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
10 <requirement type="package" version="0.9.0">seaborn</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
11 <requirement type="package" version="1.0.3">pandas</requirement>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
12 </requirements>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
13 <command>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
14 #set controls=[]
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
15 #for $input in $control#
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
16 $controls.extend([str($input.element_identifier),str($input)])
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
17 #end for#
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
18 #set treateds=[]
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
19 #for $input in $treated#
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
20 $treateds.extend([str($input.element_identifier),str($input)])
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
21 #end for#
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
22 #if $mir_input.database == "1":
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
23 #if $f.fil == "1":
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
24 #set path=$mir_input.genome1.fields.path
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
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"
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
26 #end if
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
27 #if $f.fil == "2":
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
28 #set path=$mir_input.genome1.fields.path
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
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"
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
30 #end if
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
31 #else:
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
32 #if $f.fil == "1":
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
33 #set path=$mir_input.genome2.fields.value
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
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"
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
35 #end if
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
36 #if $f.fil == "2":
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
37 #set path=$mir_input.genome2.fields.value
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
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"
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
39 #end if
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
40 #end if
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
41
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
42 </command>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
43 <inputs>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
44 <param name="analysis" type="select" label="Discover miR with templated or/and non-templated isomiRs" help="Choose the category of miRNAs for detection">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
45 <option value="1" selected="true">Detection of only templated miRNAs</option>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
46 <option value="2">Detection of templated and non-templated miRNAs</option>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
47 </param>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
48 <conditional name="mir_input">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
49 <param name="database" type="select" label="Reference miRNA DB" help="Choose which database prefer to be used.">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
50 <option value="1" selected="true">MirBase</option>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
51 <option value="2">MirGene</option>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
52 </param>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
53 <when value="1">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
54 <param name="genome1" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest are not listed, contact the Galaxy team">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
55 <options from_data_table="mirbase" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
56 </param>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
57 </when>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
58 <when value="2">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
59 <param name="genome2" type="select" label="Reference miRNAs (organism)" help="If your genome coordinates of interest are not listed, contact the Galaxy team">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
60 <options from_data_table="mirgene" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
61 </param>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
62 </when>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
63 </conditional>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
64 <param name="fal1" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
65 <param name="control" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
66 <param name="fal2" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor', 'normal', 'treated' or 'control'"/>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
67 <param name="treated" format="sam" type="data" multiple="True" label="Select BAM files of the factor level samples" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
68 <conditional name="f">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
69 <param name="fil" type="select" label="Filter low counts" help="Treat genes with very low expression as unexpressed and filter out">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
70 <option value="1" selected="true">No</option>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
71 <option value="2">Yes</option>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
72 </param>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
73 <when value="2">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
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"/>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
75 <param name="fil2" type="integer" value="0" label="Minimum counts" help="Filter out all genes that do not meet this minimum count"/>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
76 </when>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
77 <when value="1">
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
78 </when>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
79 </conditional>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
80 <param name="db" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Database files" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
81 <param name="cmatrix" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Output Matrix files, one for each factor level" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
82 <param name="c_files" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Output Count tables, one for each sample" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
83 </inputs>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
84 <outputs>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
85 <collection name="list_output1" type="list" label="Database ${fal1} templated" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
86 <discover_datasets pattern="__name__" format="tabular" directory="split1" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
87 <filter>db == 1 and (analysis == "1" or analysis == "2")</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
88 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
89 <collection name="list_output2" type="list" label="Database ${fal2} templated" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
90 <discover_datasets pattern="__name__" format="tabular" directory="split2" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
91 <filter>db == 1 and (analysis == "1" or analysis == "2")</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
92 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
93 <collection name="list_output3" type="list" label="Database ${fal1} non-templated" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
94 <discover_datasets pattern="__name__" format="tabular" directory="split3" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
95 <filter>db == 1 and analysis == "2"</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
96 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
97 <collection name="list_output4" type="list" label="Database ${fal2} non-templated" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
98 <discover_datasets pattern="__name__" format="tabular" directory="split4" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
99 <filter>db == 1 and analysis == "2"</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
100 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
101
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
102 <collection name="Counts" type="list" label="Count Matrices" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
103 <discover_datasets pattern="__name__" format="tabular" directory="Counts" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
104 <filter>cmatrix==1</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
105 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
106 <collection name="list_output9" type="list" label="Count files ${fal1} for Differential Expression" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
107 <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_con" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
108 <filter>c_files==1 and (analysis == "1")</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
109 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
110 <collection name="list_output10" type="list" label="Count files ${fal2} for Differential Expression" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
111 <discover_datasets pattern="__name__" format="tabular" directory="Diff/temp_tre" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
112 <filter>c_files==1 and (analysis == "1")</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
113 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
114 <collection name="list_output11" type="list" label="Count files ${fal1} for Differential Expression" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
115 <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_con" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
116 <filter>c_files==1 and analysis == "2"</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
117 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
118 <collection name="list_output12" type="list" label="Count files ${fal2} for Differential Expression" >
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
119 <discover_datasets pattern="__name__" format="tabular" directory="Diff/n_temp_tre" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
120 <filter>c_files==1 and analysis == "2"</filter>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
121 </collection>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
122
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
123 <data name="Results non templated treated1" format="pdf" label="IsomiR Profile Report" from_work_dir="$__tool_directory__/report1.pdf" />
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
124 </outputs>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
125 <help>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
126 </help>
63ae92b7f425 Uploaded
glogobyte
parents:
diff changeset
127 </tool>