annotate macros.xml @ 20:e4691e1589d3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 59d42345d86e33e01aa50013f00f4dc0612d3de8
author iuc
date Mon, 08 Apr 2019 13:49:22 -0400
parents 49370cb85f0f
children 093678460093
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1 <macros>
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2
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3 <token name="@read1_options@"><![CDATA[
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4
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5 ## Read1 trimming
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6
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7 #for $a in $library.r1.adapters
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8 #if $a.adapter_source.adapter_source_list == 'builtin':
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9 -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}'
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10 #else if $a.adapter_source.adapter_source_list == 'file':
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11 -a file:'${a.adapter_source.adapter_file}'
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12 #else if str($a.adapter_source.adapter_name) != "":
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13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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14 #else
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15 -a '${a.adapter_source.adapter}'
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16 #end if
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17 #end for
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18 #for $aa in $library.r1.anywhere_adapters
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19 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
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20 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}'
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21 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
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22 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}'
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23 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
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24 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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25 #else
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26 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
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27 #end if
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28 #end for
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29 #for $fa in $library.r1.front_adapters
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30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
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31 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}'
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32 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
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33 -g file:'${fa.front_adapter_source.front_adapter_file}'
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34 #else if str($fa.front_adapter_source.front_adapter_name) != "":
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35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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36 #else
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37 -g '${fa.front_adapter_source.front_adapter}'
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38 #end if
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39 #end for
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40
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41 #if str($library.r1.cut) != '0':
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42 -u $library.r1.cut
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43 #end if
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44
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45 ## Additional Outputs
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46
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47 #if $output_options.info_file:
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48 --info-file=$info_file
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49 #end if
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50 #if $output_options.rest_file:
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51 --rest-file='${rest_output}'
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52 #end if
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53 #if $output_options.wildcard_file:
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54 --wildcard-file='${wild_output}'
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55 #end if
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56 #if $output_options.too_short_file:
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57 --too-short-output='${too_short_output}'
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58 #end if
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59 #if $output_options.too_long_file:
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60 --too-long-output='${too_long_output}'
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61 #end if
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62 #if $output_options.untrimmed_file:
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63 --untrimmed-output='${untrimmed_output}'
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64 #end if
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65
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66 ]]></token>
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67
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68 <token name="@read2_options@"><![CDATA[
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69
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70 ## Read2 trimming
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71
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72 #for $a in $library.r2.adapters2
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73 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
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74 -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}'
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75 #else if $a.adapter_source2.adapter_source_list2 == 'file':
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76 -A file:'${a.adapter_source2.adapter_file2}'
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77 #else if str($a.adapter_source2.adapter_name2) != "":
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78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
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79 #else
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80 -A '${a.adapter_source2.adapter2}'
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81 #end if
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82 #end for
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83 #for $aa in $library.r2.anywhere_adapters2
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84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
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85 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}'
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86 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
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87 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}'
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88 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
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89 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
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90 #else
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91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
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92 #end if
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93 #end for
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94 #for $fa in $library.r2.front_adapters2
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95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
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96 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}'
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97 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
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98 -G file:'${fa.front_adapter_source2.front_adapter_file2}'
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99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
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100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}'
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101 #else
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102 -G '${fa.front_adapter_source2.front_adapter2}'
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103 #end if
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104 #end for
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105
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106 #if str($library.r2.cut2) != '0':
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107 -U $library.r2.cut2
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108 #end if
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109
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110 ## Additional Outputs - Read 2
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111
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112 #if $output_options.too_short_file:
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113 --too-short-paired-output='${too_short_paired_output}'
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114 #end if
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115 #if $output_options.too_long_file:
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116 --too-long-paired-output='${too_long_paired_output}'
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117 #end if
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118 #if $output_options.untrimmed_file:
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119 --untrimmed-paired-output='${untrimmed_paired_output}'
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120 #end if
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121
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122 ]]></token>
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123
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124 <xml name="single_end_options" >
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125
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126 <section name="r1" title="Read 1 Options" expanded="True">
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127
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128 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
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129 <conditional name="adapter_source">
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130 <param name="adapter_source_list" type="select" label="Source" >
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131 <option value="builtin" selected="True">Standard (select from the list below)</option>
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132 <option value="user">Enter custom sequence</option>
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133 <option value="file">File From History</option>
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134 </param>
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135
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136 <when value="user">
16
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137 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" />
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138 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
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139 </when>
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140
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141 <when value="builtin">
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142 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter">
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143 <options from_data_table="adapters">
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144 <filter type="sort_by" column="1" />
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145 </options>
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146 </param>
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147 </when>
19
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148
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149 <when value="file">
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150 <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" />
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151 </when>
11
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152 </conditional>
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153 </repeat>
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154
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155 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
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156 <conditional name="front_adapter_source">
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157 <param name="front_adapter_source_list" type="select" label="Source">
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158 <option value="builtin" selected="True">Standard (select from the list below)</option>
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159 <option value="user">Enter custom sequence</option>
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160 <option value="file">File From History</option>
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161 </param>
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162
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163 <when value="user">
16
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164 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" />
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165 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
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166 </when>
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167 <when value="builtin">
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168 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter">
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169 <options from_data_table="adapters">
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170 <filter type="sort_by" column="1" />
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171 </options>
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172 </param>
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173 </when>
19
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174 <when value="file">
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175 <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
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176 </when>
11
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177 </conditional>
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178 </repeat>
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179
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180 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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181 <conditional name="anywhere_adapter_source">
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182 <param name="anywhere_adapter_source_list" type="select" label="Source">
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183 <option value="builtin" selected="True">Standard (select from the list below)</option>
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184 <option value="user">Enter custom sequence</option>
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185 <option value="file">File From History</option>
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186 </param>
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187
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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188 <when value="user">
16
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189 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" />
11
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190 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
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191 </when>
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192 <when value="builtin">
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193 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter">
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194 <options from_data_table="adapters">
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195 <filter type="sort_by" column="1" />
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196 </options>
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197 </param>
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198 </when>
19
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199 <when value="file">
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200 <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
49370cb85f0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
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201 </when>
11
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202 </conditional>
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203 </repeat>
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204
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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205 <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." />
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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206
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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207 </section>
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208
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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209 </xml>
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210
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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211 <xml name="paired_end_options" >
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212
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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213 <!-- Read 1 Options -->
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214 <expand macro="single_end_options" />
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215
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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216 <!-- Read 2 Options -->
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217 <section name="r2" title="Read 2 Options" expanded="True">
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218
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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219 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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220 <conditional name="adapter_source2">
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221 <param name="adapter_source_list2" type="select" label="Source" >
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222 <option value="builtin" selected="True">Standard (select from the list below)</option>
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223 <option value="user">Enter custom sequence</option>
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224 <option value="file">File From History</option>
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225 </param>
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226
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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227 <when value="user">
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228 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
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229 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
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230 </when>
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231
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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232 <when value="builtin">
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233 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter">
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234 <options from_data_table="adapters">
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235 <filter type="sort_by" column="1" />
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236 </options>
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237 </param>
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238 </when>
19
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239 <when value="file">
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240 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' adapters" />
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241 </when>
11
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242 </conditional>
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243 </repeat>
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244
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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245 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
8665bcc8b847 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
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246 <conditional name="front_adapter_source2">
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247 <param name="front_adapter_source_list2" type="select" label="Source">
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248 <option value="builtin" selected="True">Standard (select from the list below)</option>
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249 <option value="user">Enter custom sequence</option>
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250 <option value="file">File From History</option>
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251 </param>
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252
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253 <when value="user">
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254 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
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255 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
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256 </when>
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257 <when value="builtin">
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258 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter">
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259 <options from_data_table="adapters">
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260 <filter type="sort_by" column="1" />
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261 </options>
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262 </param>
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263 </when>
19
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264 <when value="file">
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265 <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
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266 </when>
11
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267 </conditional>
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268 </repeat>
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269
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270 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
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271 <conditional name="anywhere_adapter_source2">
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272 <param name="anywhere_adapter_source_list2" type="select" label="Source">
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273 <option value="builtin" selected="True">Standard (select from the list below)</option>
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274 <option value="user">Enter custom sequence</option>
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275 <option value="file">File From History</option>
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276 </param>
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277
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278 <when value="user">
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279 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
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280 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />
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281 </when>
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282 <when value="builtin">
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283 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter">
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284 <options from_data_table="adapters">
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285 <filter type="sort_by" column="1" />
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286 </options>
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287 </param>
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288 </when>
19
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289 <when value="file">
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290 <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
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291 </when>
11
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292 </conditional>
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293 </repeat>
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294
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295 <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." />
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296
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297 </section>
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298
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299 </xml>
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300
12
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301 <xml name="inherit_format_1">
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302 <actions>
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303 <conditional name="library.type">
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304 <when value="single">
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305 <action type="format">
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306 <option type="from_param" name="library.input_1" param_attribute="ext" />
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307 </action>
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308 </when>
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309 <when value="paired">
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310 <action type="format">
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311 <option type="from_param" name="library.input_1" param_attribute="ext" />
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312 </action>
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313 </when>
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314 <when value="paired_collection">
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315 <action type="format">
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316 <option type="from_param" name="library.input_1" param_attribute="forward.ext" />
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317 </action>
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318 </when>
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319 </conditional>
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320 </actions>
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321 </xml>
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322
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323 <xml name="inherit_format_2">
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324 <actions>
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325 <conditional name="library.type">
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326 <when value="paired">
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327 <action type="format">
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328 <option type="from_param" name="library.input_2" param_attribute="ext" />
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329 </action>
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330 </when>
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331 <when value="paired_collection">
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332 <action type="format">
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333 <option type="from_param" name="library.input_1" param_attribute="reverse.ext" />
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334 </action>
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335 </when>
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336 </conditional>
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337 </actions>
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338 </xml>
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339
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340 </macros>