Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 8:9750f8c1d3cb draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty
author yhoogstrate
date Tue, 04 Aug 2015 09:43:29 -0400
parents 39d95e2675f5
children 0cae6e3273a8
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1 <tool id="crossmap" name="CrossMap" version="0.1.9">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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4 <requirements>
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5 <requirement type="package" version="0.1.9">crossmap</requirement>
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6 </requirements>
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8 <stdio>
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9 <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
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10 <regex match="^@ " source="stdin" level="warning" />
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11 </stdio>
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12
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13 <command>
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14 CrossMap.py
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15 $multiple.input_format
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17 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
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18 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
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19 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
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20 #else
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21 "$multiple.seq_source.input_chain"
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22 #end if
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23
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24 <!-- these arguments don't work
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25 #if $multiple.input_format == "bam"
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26 -m $multiple.insert_size
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27 -s $multiple.insert_size_stdev
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28 -t $multiple.insert_size_fold
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29 #end if
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30 -->
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32 "$multiple.seq_source.input"
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34 #if $multiple.input_format == "vcf"
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35 "$multiple.seq_source.input_fasta"
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36 #end if
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37
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38 $output
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39 </command>
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40
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41 <inputs>
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42 <conditional name="multiple">
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43 <param name="input_format" type="select" label="Convert a file of the following format">
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44 <option value="bam">BAM or SAM format</option>
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45 <option value="bed">BED or BED-like</option>
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46 <option value="bigwig">BigWig</option>
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47 <option value="gff">GFF or GTF</option>
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48 <option value="vcf">VCF</option>
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49 <option value="wig">Wiggle or bedGraph</option>
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50 </param>
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51 <when value="bam">
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52 <conditional name="seq_source">
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53 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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54 <option value="cached">Local data (in galaxy)</option>
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55 <option value="history">From History</option>
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56 </param>
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57 <when value="cached">
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58 <param type="data" format="bam,sam" name="input" label="BAM/SAM file">
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59 <validator type="unspecified_build" />
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60 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
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61 </param>
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62 <param name="input_chain" type="select" label="Lift Over To">
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63 <options from_file="liftOver.loc">
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64 <column name="name" index="1"/>
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65 <column name="value" index="2"/>
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66 <column name="dbkey" index="0"/>
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67 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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68 </options>
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69 </param>
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70 </when>
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71 <when value="history">
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72 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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73 <param type="data" name="input_chain" label="LiftOver chain file" />
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74 </when>
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75 </conditional>
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76
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77 <!-- These parameters don't work
5
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78 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
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79 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
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80 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
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81 -->
5
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82 </when>
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83 <when value="bed">
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84 <conditional name="seq_source">
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85 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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86 <option value="cached">Local data (in galaxy)</option>
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87 <option value="history">From History</option>
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88 </param>
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89 <when value="cached">
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90 <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.">
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91 <validator type="unspecified_build" />
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92 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
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93 </param>
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94 <param name="input_chain" type="select" label="Lift Over To">
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95 <options from_file="liftOver.loc">
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96 <column name="name" index="1"/>
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97 <column name="value" index="2"/>
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98 <column name="dbkey" index="0"/>
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99 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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100 </options>
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101 </param>
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102 </when>
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103 <when value="history">
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104 <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
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105 <param type="data" name="input_chain" label="LiftOver chain file" />
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106 </when>
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107 </conditional>
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108 </when>
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109 <when value="bigwig">
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110 <conditional name="seq_source">
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111 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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112 <option value="cached">Local data (in galaxy)</option>
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113 <option value="history">From History</option>
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114 </param>
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115 <when value="cached">
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116 <param format="bigwig" name="input" type="data" label="BigWig file">
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117 <validator type="unspecified_build" />
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118 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
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119 </param>
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120 <param name="input_chain" type="select" label="Lift Over To">
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121 <options from_file="liftOver.loc">
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122 <column name="name" index="1"/>
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123 <column name="value" index="2"/>
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124 <column name="dbkey" index="0"/>
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125 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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126 </options>
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127 </param>
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128 </when>
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129 <when value="history">
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130 <param format="bigwig" name="input" type="data" label="BigWig file" />
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131 <param type="data" name="input_chain" label="LiftOver chain file" />
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132 </when>
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133 </conditional>
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134 </when>
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135 <when value="gff">
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136 <conditional name="seq_source">
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137 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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138 <option value="cached">Local data (in galaxy)</option>
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139 <option value="history">From History</option>
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140 </param>
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141 <when value="cached">
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142 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
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143 <validator type="unspecified_build" />
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144 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
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145 </param>
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146 <param name="input_chain" type="select" label="Lift Over To">
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147 <options from_file="liftOver.loc">
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148 <column name="name" index="1"/>
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149 <column name="value" index="2"/>
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150 <column name="dbkey" index="0"/>
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151 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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152 </options>
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153 </param>
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154 </when>
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155 <when value="history">
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156 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file" />
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157 <param type="data" name="input_chain" label="LiftOver chain file" />
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158 </when>
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159 </conditional>
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160 </when>
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161 <when value="vcf">
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162 <conditional name="seq_source">
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163 <param name="index_source" type="select" label="Source for LiftOver Data">
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164 <option value="cached">Local data (in galaxy)</option>
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165 <option value="history_chain">Chain file from History</option>
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166 <option value="history_all">Chain &amp; FASTA files from History</option>
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167 </param>
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168 <when value="cached">
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169 <param type="data" format="vcf" name="input" label="VCF file">
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170 <validator type="unspecified_build" />
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171 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
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172 </param>
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173
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174 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
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175 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
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176 <options from_file="liftOver.loc">
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177 <column name="name" index="1" />
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178 <column name="value" index="1" /><!-- It is not possible to send the *.chain file as value, and obtain the 2nd dbkey as parameter via a filter -->
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179 <column name="dbkey" index="0" />
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180 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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181 </options>
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182 </param>
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183
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184 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
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185 <options from_file="all_fasta.loc">
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186 <column name="name" index="2"/>
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187 <column name="value" index="3"/>
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188 <column name="dbkey" index="1"/>
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189 <filter type="param_value" ref="input_chain" column="1" />
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190 </options>
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191 </param>
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192 </when>
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193
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194 <when value="history_chain">
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195 <param type="data" format="vcf" name="input" label="VCF file">
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196 <validator type="unspecified_build" />
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197 <validator type="dataset_metadata_in_file" filename="all_fasta.loc" metadata_name="dbkey" metadata_column="1" message="LiftOver mapping (FASTA file) is not available for the specified build." />
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198 </param>
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199 <param type="data" name="input_chain" multiple="false" label="LiftOver chain file" />
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200 <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
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201 <options from_file="all_fasta.loc">
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202 <column name="name" index="2"/>
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203 <column name="value" index="3"/>
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204 <column name="dbkey" index="1"/>
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205 </options>
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206 </param>
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207 </when>
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208
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209 <when value="history_all">
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210 <param type="data" format="vcf" name="input" label="VCF file" />
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211 <param type="data" name="input_all_chain" multiple="false" label="LiftOver chain file" />
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212 <param type="data" format="fasta" name="input_all_fasta" multiple="false" label="Full genome FASTA file" />
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213 </when>
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214 </conditional>
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215 </when>
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216 <when value="wig">
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217 <conditional name="seq_source">
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218 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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219 <option value="cached">Local data (in galaxy)</option>
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220 <option value="history">From History</option>
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221 </param>
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222 <when value="cached">
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223 <param format="wig" name="input" type="data" label="Wiggle file">
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224 <validator type="unspecified_build" />
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225 <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build." />
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226 </param>
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227 <param name="input_chain" type="select" label="Lift Over To">
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228 <options from_file="liftOver.loc">
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229 <column name="name" index="1"/>
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230 <column name="value" index="2"/>
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231 <column name="dbkey" index="0"/>
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232 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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233 </options>
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234 </param>
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235 </when>
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236 <when value="history">
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237 <param format="wig" name="input" type="data" label="Wiggle file" />
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238 <param type="data" name="input_chain" label="LiftOver chain file" />
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239 </when>
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240 </conditional>
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241 </when>
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242 </conditional>
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243 </inputs>
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244
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245 <outputs>
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246 <data format="text" name="output" label="${tool.name} on ${input.hid}: ${input.name}" />
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247 </outputs>
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248
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249 <tests>
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250 <test>
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251 <param name="input" value="test1.hg19.txt"/>
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252 <param name="input" value="hg18tohg19.chain"/>
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253 <output name="output" file="test1.hg18.txt"/>
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254 </test>
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255 </tests>
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256
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257 <help>
5
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258 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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259 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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260 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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261 and VCF, reading from remote servers and file compression are supported.
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262
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263 CrossMap bed
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264 ------------
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265 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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266 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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267
1
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268 </help>
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269
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270 <citations>
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271 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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272 </citations>
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273 </tool>