Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 9:0cae6e3273a8 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd
author yhoogstrate
date Wed, 05 Aug 2015 02:58:35 -0400
parents 9750f8c1d3cb
children a5eb1023fc34
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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="both" level="log" description="tool progress"/>
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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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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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38 <!-- BED format does not write to the output file, but does write fails to stdout -->
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39 > "$output"
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41 2>/dev/null
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42 </command>
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43
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44 <inputs>
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45 <conditional name="multiple">
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46 <param name="input_format" type="select" label="Convert a file of the following format">
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47 <option value="bam">BAM or SAM format</option>
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48 <option value="bed">BED or BED-like</option>
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49 <option value="bigwig">BigWig</option>
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50 <option value="gff">GFF or GTF</option>
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51 <option value="vcf">VCF</option>
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52 <option value="wig">Wiggle or bedGraph</option>
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53 </param>
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54 <when value="bam">
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55 <conditional name="seq_source">
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56 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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57 <option value="cached">Local data (in galaxy)</option>
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58 <option value="history">From History</option>
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59 </param>
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60 <when value="cached">
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61 <param type="data" format="bam,sam" name="input" label="BAM/SAM file">
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62 <validator type="unspecified_build" />
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63 <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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64 </param>
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65 <param name="input_chain" type="select" label="Lift Over To">
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66 <options from_file="liftOver.loc">
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67 <column name="name" index="1"/>
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68 <column name="value" index="2"/>
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69 <column name="dbkey" index="0"/>
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70 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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71 </options>
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72 </param>
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73 </when>
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74 <when value="history">
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75 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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76 <param type="data" name="input_chain" label="LiftOver chain file" />
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77 </when>
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78 </conditional>
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79
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80 <!-- These parameters don't work
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81 <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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82 <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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83 <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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84 -->
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85 </when>
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86 <when value="bed">
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87 <conditional name="seq_source">
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88 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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89 <option value="cached">Local data (in galaxy)</option>
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90 <option value="history">From History</option>
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91 </param>
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92 <when value="cached">
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93 <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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94 <validator type="unspecified_build" />
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95 <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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96 </param>
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97 <param name="input_chain" type="select" label="Lift Over To">
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98 <options from_file="liftOver.loc">
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99 <column name="name" index="1"/>
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100 <column name="value" index="2"/>
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101 <column name="dbkey" index="0"/>
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102 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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103 </options>
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104 </param>
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105 </when>
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106 <when value="history">
9
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107 <param type="data" format="bed" name="input" 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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108 <param type="data" name="input_chain" label="LiftOver chain file" />
5
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109 </when>
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110 </conditional>
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111 </when>
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112 <when value="bigwig">
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113 <conditional name="seq_source">
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114 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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115 <option value="cached">Local data (in galaxy)</option>
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116 <option value="history">From History</option>
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117 </param>
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118 <when value="cached">
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119 <param format="bigwig" name="input" type="data" label="BigWig file">
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120 <validator type="unspecified_build" />
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121 <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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122 </param>
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123 <param name="input_chain" type="select" label="Lift Over To">
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124 <options from_file="liftOver.loc">
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125 <column name="name" index="1"/>
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126 <column name="value" index="2"/>
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127 <column name="dbkey" index="0"/>
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128 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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129 </options>
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130 </param>
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131 </when>
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132 <when value="history">
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133 <param format="bigwig" name="input" type="data" label="BigWig file" />
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134 <param type="data" name="input_chain" label="LiftOver chain file" />
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135 </when>
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136 </conditional>
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137 </when>
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138 <when value="gff">
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139 <conditional name="seq_source">
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140 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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141 <option value="cached">Local data (in galaxy)</option>
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142 <option value="history">From History</option>
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143 </param>
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144 <when value="cached">
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145 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
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146 <validator type="unspecified_build" />
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147 <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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148 </param>
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149 <param name="input_chain" type="select" label="Lift Over To">
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150 <options from_file="liftOver.loc">
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151 <column name="name" index="1"/>
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152 <column name="value" index="2"/>
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153 <column name="dbkey" index="0"/>
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154 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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155 </options>
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156 </param>
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157 </when>
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158 <when value="history">
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159 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file" />
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160 <param type="data" name="input_chain" label="LiftOver chain file" />
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161 </when>
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162 </conditional>
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163 </when>
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164 <when value="vcf">
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165 <conditional name="seq_source">
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166 <param name="index_source" type="select" label="Source for LiftOver Data">
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167 <option value="cached">Local data (in galaxy)</option>
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168 <option value="history_chain">Chain file from History</option>
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169 <option value="history_all">Chain &amp; FASTA files from History</option>
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170 </param>
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171 <when value="cached">
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172 <param type="data" format="vcf" name="input" label="VCF file">
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173 <validator type="unspecified_build" />
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174 <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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175 </param>
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176
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177 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
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178 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
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179 <options from_file="liftOver.loc">
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180 <column name="name" index="1" />
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181 <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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182 <column name="dbkey" index="0" />
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183 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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184 </options>
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185 </param>
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186
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187 <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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188 <options from_file="all_fasta.loc">
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189 <column name="name" index="2"/>
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190 <column name="value" index="3"/>
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191 <column name="dbkey" index="1"/>
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192 <filter type="param_value" ref="input_chain" column="1" />
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193 </options>
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194 </param>
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195 </when>
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196
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197 <when value="history_chain">
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198 <param type="data" format="vcf" name="input" label="VCF file">
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199 <validator type="unspecified_build" />
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200 <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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201 </param>
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202 <param type="data" name="input_chain" multiple="false" label="LiftOver chain file" />
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203 <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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204 <options from_file="all_fasta.loc">
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205 <column name="name" index="2"/>
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206 <column name="value" index="3"/>
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207 <column name="dbkey" index="1"/>
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208 </options>
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209 </param>
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210 </when>
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211
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212 <when value="history_all">
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213 <param type="data" format="vcf" name="input" label="VCF file" />
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214 <param type="data" name="input_all_chain" multiple="false" label="LiftOver chain file" />
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215 <param type="data" format="fasta" name="input_all_fasta" multiple="false" label="Full genome FASTA file" />
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216 </when>
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217 </conditional>
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218 </when>
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219 <when value="wig">
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220 <conditional name="seq_source">
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221 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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222 <option value="cached">Local data (in galaxy)</option>
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223 <option value="history">From History</option>
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224 </param>
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225 <when value="cached">
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226 <param format="wig" name="input" type="data" label="Wiggle file">
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227 <validator type="unspecified_build" />
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228 <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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229 </param>
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230 <param name="input_chain" type="select" label="Lift Over To">
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231 <options from_file="liftOver.loc">
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232 <column name="name" index="1"/>
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233 <column name="value" index="2"/>
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234 <column name="dbkey" index="0"/>
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235 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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236 </options>
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237 </param>
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238 </when>
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239 <when value="history">
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240 <param format="wig" name="input" type="data" label="Wiggle file" />
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241 <param type="data" name="input_chain" label="LiftOver chain file" />
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242 </when>
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243 </conditional>
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244 </when>
1
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245 </conditional>
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246 </inputs>
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247
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248 <outputs>
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249 <data format="text" name="output" label="${tool.name} on " />
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250 </outputs>
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251
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252 <tests>
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253 <test>
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254 <param name="input" value="test1.hg19.txt"/>
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255 <param name="input" value="hg18tohg19.chain"/>
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256 <output name="output" file="test1.hg18.txt"/>
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257 </test>
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258 </tests>
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259
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260 <help>
5
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261 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
1
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262 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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263 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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264 and VCF, reading from remote servers and file compression are supported.
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265
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266 CrossMap bed
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267 ------------
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268 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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269 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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270
1
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271 </help>
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272
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273 <citations>
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274 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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275 </citations>
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276 </tool>