Mercurial > repos > iuc > raceid_inspecttrajectory

annotate macros.xml @ 10:6e90c8adf84f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 0ffa71ef9f8d020fe7ba94502db8cec26fd8741f
author iuc
date Tue, 05 Nov 2024 16:33:56 +0000
parents a6821f856a1e
children
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e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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1 <macros>
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2 <token name="@STRING2VECTOR@">
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3 string2numericvector = function(string){
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4 #' Converts a string to a valid vector
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5 #'
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6 #' e.g. "-1,2:5,2" evaluates to c(-1,2,3,4,5,2)
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7 #'
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8 #' @param add string2vector function to safe environment
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9 #' @return vector of integers
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10 terms = unlist(strsplit(string, split=","))
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11 res = lapply(terms, function(x){
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12 if (grepl(":",x)){
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13 l_r = as.integer(c(unlist(strsplit(x,split=":"))))
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14 return(seq(l_r[1],l_r[2]))
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15 }
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16 return(as.integer(x))
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17 })
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18 return(c(unlist(res)))
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19 }
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20
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21 string2textvector = function(string){
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22 #' Converts a string to a valid string vector
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23 #'
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24 #' e.g. "red,yellow,white" evaluates to c("red","yellow","white")
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25 return(unlist(strsplit(string,",")))
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26 }
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27 </token>
7
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28 <token name="@TOOL_VERSION@">0.2.3</token>
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29 <token name="@VERSION_SUFFIX@">3</token>
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30 <token name="@PROFILE@">21.01</token>
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31
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32 <macro name="version_command_config" token_prog="temp" token_cheetah="temp2" token_out="2&#62; '$outlog'">
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33 <version_command><![CDATA[
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34 Rscript '$__tool_directory__/scripts/@PROG@' 2>&1 | head -1 | cut -d' ' -f 2
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35 ]]></version_command>
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36 <command detect_errors="exit_code"><![CDATA[
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37 Rscript '$__tool_directory__/scripts/@PROG@' '$userconf' @OUT@
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38 ]]>
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39 </command>
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40 <configfiles>
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41 <configfile name="userconf" ><![CDATA[
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42 @STRING2VECTOR@
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43
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44 @@CHEETAH@@
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45 ]]></configfile>
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46 </configfiles>
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47 </macro>
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48
0
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49 <macro name="requirements" >
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50 <requirements>
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51 <requirement type="package" version="@TOOL_VERSION@" >r-raceid</requirement>
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52 <!-- <requirement type="package" version="1.6.2">bioconductor-scran</requirement> -->
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53 </requirements>
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54 </macro>
10
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55 <xml name="bio_tools">
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56 <xrefs>
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57 <xref type="bio.tools">RaceID</xref>
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58 </xrefs>
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59 </xml>
0
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60 <macro name="yesno_checkedno" >
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61 <option value="yes" >Yes</option>
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62 <option value="no" selected="true" >No</option>
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63 </macro>
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64 <macro name="use_defaults_no" >
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65 <conditional name="use" >
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66 <param name="def" type="select" label="Use Defaults?" >
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67 <option value="yes" selected="true" >Yes</option>
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68 <option value="no" >No</option>
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69 </param>
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70 <when value="yes" />
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71 <when value="no" >
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72 <yield />
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73 </when>
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74 </conditional>
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75 </macro>
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76 <macro name="test_nondef" >
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77 <conditional name="use" >
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78 <param name="def" value="no" />
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79 <yield />
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80 </conditional>
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81 </macro>
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82 <macro name="section_test_nondef" >
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83 <section name="@SECTIONNAME@" >
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84 <expand macro="test_nondef" >
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85 <yield />
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86 </expand>
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87 </section>
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88 </macro>
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89 <macro name="citations" >
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90 <citations>
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91 <citation type="doi">10.1038/nature14966</citation>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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92 <citation type="doi">10.1038/nmeth.4662</citation>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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93 </citations>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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94 </macro>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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95 <!-- Sanitizers -->
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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96 <macro name="sanitize_title">
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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97 <sanitizer invalid_char="">
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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98 <valid initial="string.letters,string.digits" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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99 <add value=" " />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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100 <add value="_" />
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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101 </valid>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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102 </sanitizer>
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iuc
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103 </macro>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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104 <macro name="sanitize_regex" >
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
iuc
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105 <sanitizer invalid_char="">
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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106 <valid initial="string.letters,string.digits">
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iuc
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107 <add value="!"/>
e0e9b24d76aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit f880060c478d42202df5b78a81329f8af56b1138
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108 <add value="="/>
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109 <add value="-"/>
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110 <add value="."/>
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111 <add value="*"/>
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iuc
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112 <add value="?"/>
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iuc
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113 <add value="+"/>
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iuc
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114 <add value="\\"/>
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115 <add value="_"/>
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iuc
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116 <add value="|"/>
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117 <add value="&#91;"/> <!-- left square bracket, e.g subselecting from vec[1] -->
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iuc
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118 <add value="&#93;"/> <!-- right square bracket -->
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iuc
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119 <add value="&#40;"/> <!-- left parenthesis -->
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iuc
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120 <add value="&#41;"/> <!-- right parenthesis -->
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121 </valid>
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122 </sanitizer>
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123 </macro>
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124 <macro name="sanitize_numeric_vector" >
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125 <sanitizer invalid_char="">
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126 <valid initial="string.digits">
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127 <add value=","/>
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128 </valid>
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129 </sanitizer>
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130 </macro>
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131 <macro name="sanitize_string_vector" >
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132 <sanitizer invalid_char="">
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133 <valid initial="string.letters,string.digits">
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134 <add value=","/>
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135 <add value="_"/>
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136 <add value="-"/>
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iuc
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137 <add value="."/>
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138 </valid>
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139 </sanitizer>
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140 </macro>
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141 </macros>