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annotate unafold.xml @ 1:3e71be1681bc draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea
author yhoogstrate
date Wed, 24 Feb 2016 11:46:13 -0500
parents 30a8e44dc6dd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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30a8e44dc6dd planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 84b70c01144fa018db45215941fb395798376100-dirty
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1 <?xml version="1.0"?>
1
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2 <tool id="unafold" name="UNAFold" version="1.1.0">
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3 <description>UNAFold RNA and DNA structure prediction</description>
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5 <requirements>
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6 <requirement type="package" version="3.8">unafold</requirement>
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7 </requirements>
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8
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9 <stdio>
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10 <regex match="mv: cannot stat ..: No such file or directory" source="stderr" level="fatal" description="Could not find CT output file\n" />
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11 </stdio>
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13 <version_command>UNAFold.pl --version</version_command>
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15 <command><![CDATA[
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16 #if str($input_source.select_fasta) == "false"
3e71be1681bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea
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17 echo ">Sequence" > "input.fasta" &&
3e71be1681bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea
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18 echo "${input_source.input_sequence}" >> "input.fasta" &&
3e71be1681bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea
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19 #end if
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21 UNAFold.pl
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22 -n $n.a
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23 -t $temp
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24 #if $n.a == "DNA"
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25 -N $sodium
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26 -M $magnesium
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27 #end if
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29 #if str($input_source.select_fasta) == "false"
3e71be1681bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea
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30 "input.fasta"
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31 #else
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32 "${input_source.input_file}"
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33 #end if
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34 &&
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35
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36 output=\$(ls | grep \.ct | sort -r | head -n 1) &&
3e71be1681bc planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/unafold_galaxy_wrapper commit 3d01452f19416679047a05e4c0a05c15d11f34ea
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37
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38 mv "\$output" "$output_ct"
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39 ]]></command>
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41 <inputs>
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42 <conditional name="input_source">
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43 <param name="select_fasta" type="boolean" truevalue="true" falsevalue="false" label="Input from FASTA file" selected="false" />
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44
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45 <when value="true">
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46 <param format="fasta" name="input_file" type="data" label="Input sequence (FASTA)"/>
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47 </when>
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48 <when value="false">
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49 <param name="input_sequence" type="text" label="Input sequence"/>
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50 </when>
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51 </conditional>
0
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52
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53 <conditional name="n">
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54 <param name="a" type="select" label="Nucleic Acid Type">
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55 <option value="RNA" selected="true">RNA</option>
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56 <option value="DNA">DNA</option>
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57 </param>
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58
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59 <when value="RNA">
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60 </when>
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61 <when value="DNA">
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62 <param name="sodium" type="float" size="6" value="1.0" min="0" max="100" label="[Na+] in M"/>
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63 <param name="magnesium" type="float" size="6" value="0.0" min="0" max="100" label="[Mg++] in M"/>
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64 </when>
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65 </conditional>
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66
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67 <param name="temp" type="integer" size="3" value="37" min="0" max="100" label="Temperature (&#176;C)"/>
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68 </inputs>
1
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69
0
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70 <outputs>
1
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71 <data format="ct" name="output_ct" label="${tool.name}"/>
0
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72 </outputs>
1
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73
0
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74 <tests>
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75 <test>
1
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76 <param name="select_fasta" value="true" />
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77 <param name="input_file" value="test1_input.fa" ftype="fasta" />
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78 <param name="temp" value="37" />
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79
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80 <output name="output_ct" file="test1_output.ct" />
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81 </test>
1
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82 <test>
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83 <param name="select_fasta" value="false" />
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84 <param name="input_sequence" value="GGGGGaaaCCCCC" />
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85 <param name="temp" value="37" />
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87 <output name="output_ct" file="test1_output.ct" lines_diff="2" /><!-- Sequence name (header) differs -->
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88 </test>
0
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89 </tests>
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90
1
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91 <help><![CDATA[
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92 ``Usage: UNAFold.pl [options] file [file]``
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93
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94 ``Options:``
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95 ``-V, --version``
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96
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97 ``-h, --help``
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98
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99 ``-n, --NA=(RNA | DNA) (defaults to RNA)``
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100
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101 ``-t, --temp=<temperature> (defaults to 37)``
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102
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103 ``-N, --sodium=<[Na+] in M> (defaults to 1)``
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104
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105 ``-M, --magnesium=<[Mg++] in M> (defaults to 0)``
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106
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107 ``-p, --polymer``
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108
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109 ``-C, --Ct=<total strand concentration>``
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110
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111 ``-I, --noisolate``
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112
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113 ``-m, --maxbp=<maximum basepair distance>``
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114
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115 ``-c, --constraints=<name of constraints file> (defaults to prefix.aux)``
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116
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117 ``-P, --percent=<energy increment percent> (defaults to 5)``
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118
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119 ``-W, --window=<window size> (default set by sequence length)``
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120
1
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121 ``-X, --max=<maximum number of foldings> (defaults to 100)``
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122
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123 ``--ann=(none | p-num | ss-count) (defaults to none)``
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124
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125 ``--mode=(auto | bases | lines) (defaults to auto)``
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126
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127 ``--label=<base numbering frequency>``
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128
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129 ``--rotate=<structure rotation angle>``
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130
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131 ``--run-type=(text | html) (defaults to text)``
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132
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133 ``--model=(EM | PF) (defaults to EM)``
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134
1
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135 ``--circular``
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136
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137 ``Obscure options:``
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138
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139 ``--allpairs``
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140
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141 ``--maxloop=<maximum bulge/interior loop size> (defaults to 30)``
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142
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143 ``--nodangle``
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144
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145 ``--simple``
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146
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147 ``--prefilter=<filter value>``
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148 ]]></help>
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149
0
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150 <citations>
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151 <citation type="doi">10.1007/978-1-60327-429-6_1</citation>
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152 </citations>
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153 </tool>