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