Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 37:9e99c09ebe84 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 2a0f8a26551929e52f6aea1d109b8a3bda81af8b-dirty
author yhoogstrate
date Thu, 12 Nov 2015 16:38:32 -0500
parents 47d4f148eb8c
children
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1 <tool id="crossmap" name="CrossMap" version="0.2.e">
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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="312">ucsc_tools</requirement>
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6 <requirement type="package" version="2.7">python</requirement>
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7 <requirement type="package" version="0.2">crossmap</requirement>
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8 </requirements>
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10 <stdio>
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11 <regex match="Aborted (core dumped)" source="stdout" level="fatal"/>
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12 <regex match=".*" source="both" level="log"/>
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13 <exit_code range="1:" />
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14 </stdio>
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16 <version_command>python $CROSSMAP_ROOT_DIR/bin/CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
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18 <!-- First line of CrossMap has hardcoded "#!/usr/bin/python". This makes use of Galaxy's python: -->
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19 <command><![CDATA[
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20 python \$CROSSMAP_ROOT_DIR/bin/CrossMap.py
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21 ${multiple.input_format.replace("sam","bam")}
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23 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
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24 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
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25 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
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26 #else
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27 "$multiple.seq_source.input_chain"
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28 #end if
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30 #if $multiple.input_format in ["bam", "sam"]
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31 -m $multiple.insert_size
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32 -s $multiple.insert_size_stdev
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33 -t $multiple.insert_size_fold
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34 #end if
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36 "$multiple.seq_source.input"
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38 #if $multiple.input_format == "vcf"
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39 "$multiple.seq_source.input_fasta"
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40 #end if
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42 #if str($multiple.include_fails) == "True"
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43 >
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44 #end if
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46 "$output"
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48 #if $multiple.input_format in ["bam", "sam"]
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49 && mv "${output}.${multiple.input_format}" "$output"
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50 && mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
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51 #else if $multiple.input_format in ["vcf"]
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52 && mv "${output}" "$output"
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53 && mv "${output}.unmap" "$output_unmapped"
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54 #else if $multiple.input_format in ["wig", "bigwig"]
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55 && mv "${output}.bw" "$output"
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56 && mv "${output}.sorted.bgr" "$output2"
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57 #end if
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58 ]]></command>
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59
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60 <inputs>
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61 <conditional name="multiple">
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62 <param name="input_format" type="select" label="Convert a file of the following format">
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63 <option value="bam">BAM</option>
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64 <option value="sam">SAM</option>
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65 <option value="bed">BED or BED-like</option>
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66 <option value="bigwig">BigWig</option>
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67 <option value="gff">GFF or GTF</option>
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68 <option value="vcf">VCF</option>
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69 <option value="wig">Wiggle or bedGraph</option>
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70 </param>
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71 <when value="bam">
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72 <conditional name="seq_source">
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73 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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74 <option value="cached">Local data (in galaxy)</option>
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75 <option value="history">From History</option>
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76 </param>
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77 <when value="cached">
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78 <param type="data" format="bam" name="input" label="BAM file">
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79 <validator type="unspecified_build" />
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80 <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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81 </param>
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82 <param name="input_chain" type="select" label="Lift Over To">
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83 <options from_file="liftOver.loc">
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84 <column name="name" index="1"/>
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85 <column name="value" index="2"/>
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86 <column name="dbkey" index="0"/>
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87 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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88 </options>
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89 </param>
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90 </when>
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91 <when value="history">
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92 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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93 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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94 </when>
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95 </conditional>
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96
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97 <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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98 <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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99 <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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100
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101 <param name="include_fails" type="hidden" tvalue="False" />
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102 </when>
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103 <when value="sam"><!-- BAM and SAM are exactly the same conditions, but they need to be separate to get the proper output format -->
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104 <conditional name="seq_source">
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105 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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106 <option value="cached">Local data (in galaxy)</option>
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107 <option value="history">From History</option>
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108 </param>
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109 <when value="cached">
33
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110 <param type="data" format="sam" name="input" label="SAM file">
31
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111 <validator type="unspecified_build" />
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112 <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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113 </param>
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114 <param name="input_chain" type="select" label="Lift Over To">
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115 <options from_file="liftOver.loc">
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116 <column name="name" index="1"/>
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117 <column name="value" index="2"/>
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118 <column name="dbkey" index="0"/>
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119 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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120 </options>
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121 </param>
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122 </when>
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123 <when value="history">
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124 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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125 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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126 </when>
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127 </conditional>
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128
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129 <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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130 <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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131 <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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132
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133 <param name="include_fails" type="hidden" tvalue="False" />
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134 </when>
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135 <when value="bed">
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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="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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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 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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157 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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158 </when>
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159 </conditional>
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160
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161 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
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162 </when>
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163 <when value="bigwig">
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164 <conditional name="seq_source">
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165 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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166 <option value="cached">Local data (in galaxy)</option>
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167 <option value="history">From History</option>
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168 </param>
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169 <when value="cached">
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170 <param format="bigwig" name="input" type="data" label="BigWig file">
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171 <validator type="unspecified_build" />
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172 <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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173 </param>
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174 <param name="input_chain" type="select" label="Lift Over To">
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175 <options from_file="liftOver.loc">
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176 <column name="name" index="1"/>
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177 <column name="value" index="2"/>
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178 <column name="dbkey" index="0"/>
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179 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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180 </options>
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181 </param>
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182 </when>
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183 <when value="history">
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184 <param type="data" format="bigwig" name="input" label="BigWig file" />
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185 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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186 </when>
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187 </conditional>
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188
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189 <param name="include_fails" type="hidden" tvalue="False" />
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190 </when>
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191 <when value="gff">
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192 <conditional name="seq_source">
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193 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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194 <option value="cached">Local data (in galaxy)</option>
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195 <option value="history">From History</option>
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196 </param>
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197 <when value="cached">
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198 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
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199 <validator type="unspecified_build" />
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200 <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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201 </param>
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202 <param name="input_chain" type="select" label="Lift Over To">
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203 <options from_file="liftOver.loc">
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204 <column name="name" index="1"/>
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205 <column name="value" index="2"/>
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206 <column name="dbkey" index="0"/>
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207 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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208 </options>
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209 </param>
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210 </when>
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211 <when value="history">
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212 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
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213 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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214 </when>
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215 </conditional>
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216
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217 <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')" />
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218 </when>
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219 <when value="vcf">
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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">
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222 <option value="cached">Local data (in galaxy)</option>
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223 <option value="history_chain">Chain file from History</option>
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224 <option value="history_all">Chain &amp; FASTA files from History</option>
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225 </param>
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226
13
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227 <when value="cached">
31
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228 <param type="data" format="vcf" name="input" label="VCF file">
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229 <validator type="unspecified_build" />
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230 <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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231 </param>
31
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232
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233 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
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234 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
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235 <options from_file="liftOver.loc">
31
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236 <column name="name" index="1" />
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237 <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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238 <column name="dbkey" index="0" />
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239 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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240 </options>
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241 </param>
31
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242
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243 <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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244 <options from_file="all_fasta.loc">
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245 <column name="name" index="2"/>
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246 <column name="value" index="3"/>
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247 <column name="dbkey" index="1"/>
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248 <filter type="param_value" ref="input_chain" column="1" />
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249 </options>
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250 </param>
13
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251 </when>
31
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252
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253 <when value="history_chain">
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254 <param type="data" format="vcf" name="input" label="VCF file">
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255 <validator type="unspecified_build" />
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256 <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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257 </param>
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258 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
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259 <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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260 <options from_file="all_fasta.loc">
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261 <column name="name" index="2"/>
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262 <column name="value" index="3"/>
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263 <column name="dbkey" index="1"/>
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264 </options>
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265 </param>
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266 </when>
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267
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268 <when value="history_all">
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269 <param type="data" format="vcf" name="input" label="VCF file" />
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270 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
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271 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
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272 </when>
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273 </conditional>
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274
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275 <param name="include_fails" type="hidden" tvalue="False" />
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276 </when>
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277 <when value="wig">
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278 <conditional name="seq_source">
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279 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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280 <option value="cached">Local data (in galaxy)</option>
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281 <option value="history">From History</option>
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282 </param>
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283 <when value="cached">
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284 <param format="wig" name="input" type="data" label="Wiggle file">
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285 <validator type="unspecified_build" />
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286 <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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287 </param>
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288 <param name="input_chain" type="select" label="Lift Over To">
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289 <options from_file="liftOver.loc">
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290 <column name="name" index="1"/>
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291 <column name="value" index="2"/>
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292 <column name="dbkey" index="0"/>
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293 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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294 </options>
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295 </param>
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296 </when>
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297 <when value="history">
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298 <param format="wig" name="input" type="data" label="Wiggle file" />
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299 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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300 </when>
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301 </conditional>
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302
31
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303 <param name="include_fails" type="hidden" tvalue="False" />
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304 </when>
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305 </conditional>
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306 </inputs>
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307
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308 <outputs>
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309 <data format="text" name="output" label="${tool.name} on ${on_string}">
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310 <change_format>
31
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311 <when input="multiple.input_format" value="bam" format="bam" />
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312 <when input="multiple.input_format" value="sam" format="sam" />
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313 <when input="multiple.input_format" value="bed" format="bed" />
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314 <when input="multiple.input_format" value="bigwig" format="bigwig" />
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315 <when input="multiple.input_format" value="gff" format="gff" />
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316 <when input="multiple.input_format" value="vcf" format="vcf" />
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317 <when input="multiple.input_format" value="wig" format="bigwig" />
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318 </change_format>
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319 </data>
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320
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321 <data format="text" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}">
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322 <filter>multiple['input_format'] in ["bam" , "sam" , "vcf"]</filter>
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323 <change_format>
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324 <when input="multiple.input_format" value="bam" format="bam" />
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325 <when input="multiple.input_format" value="vcf" format="vcf" />
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326 </change_format>
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327 </data>
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328 <data format="text" name="output2" label="${tool.name} (bedgraph) on ${on_string}">
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329 <filter>multiple['input_format'] in ["wig"]</filter>
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330 <change_format>
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331 <when input="multiple.input_format" value="wig" format="bedgraph" />
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332 </change_format>
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333 </data>
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334 </outputs>
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335
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336 <tests>
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337 <!-- BAM/SAM -->
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338 <test>
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339 <param name="input_format" value="bam"/>
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340 <param name="index_source" value="history"/>
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341 <param name="input" value="test_bam_01_input_a.sam" ftype="bam"/>
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342 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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343 <param name="include_fails" value="False"/>
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344
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345 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
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346 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
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347 </test>
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348
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349 <test>
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350 <param name="input_format" value="sam"/>
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351 <param name="index_source" value="history"/>
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352 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
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353 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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354 <param name="include_fails" value="False"/>
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355
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356 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
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357 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
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358 </test>
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359
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360 <!-- BED -->
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361 <test>
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362 <param name="input_format" value="bed"/>
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363 <param name="index_source" value="history"/>
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364 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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365 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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366 <param name="include_fails" value="False"/>
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367
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368 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
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369 </test>
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370 <test>
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371 <param name="input_format" value="bed"/>
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372 <param name="index_source" value="history"/>
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373 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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374 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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375 <param name="include_fails" value="True"/>
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376
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377 <output name="output" file="test_bed_01_output_a__all.bed"/>
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378 </test>
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379 <test>
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380 <param name="input_format" value="bed"/>
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381 <param name="index_source" value="history"/>
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382 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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383 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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384 <param name="include_fails" value="False"/>
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385
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386 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
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387 </test>
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388 <test>
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389 <param name="input_format" value="bed"/>
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390 <param name="index_source" value="history"/>
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391 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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392 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
13
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393 <param name="include_fails" value="True"/>
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394
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395 <output name="output" file="test_bed_02_output_a__all.bed"/>
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396 </test>
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397
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398 <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2, but patched via galaxy toolshed installer -->
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399 <test>
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400 <param name="input_format" value="bigwig"/>
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401 <param name="index_source" value="history"/>
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402 <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
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403 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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404 <param name="include_fails" value="False"/>
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405
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406 <output name="output" file="test_bigwig_01_output_a.bw"/>
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407 <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/>
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408 </test>
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409 <!-- GFF -->
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410 <test>
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411 <param name="input_format" value="gff"/>
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412 <param name="index_source" value="history"/>
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413 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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414 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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415 <param name="include_fails" value="False"/>
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416
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417 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
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418 </test>
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419 <test>
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420 <param name="input_format" value="gff"/>
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421 <param name="index_source" value="history"/>
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422 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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423 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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424 <param name="include_fails" value="True"/>
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425
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426 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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427 </test>
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428
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429 <!-- VCF -->
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430 <test>
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431 <param name="input_format" value="vcf"/>
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432 <param name="index_source" value="history_all"/>
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433 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
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434 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
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435 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
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436 <param name="include_fails" value="False"/>
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437
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438 <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/>
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439 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
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440 </test>
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441 </tests>
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442
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443 <!-- WIG - Doesn't understand fixedStep -->
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444 <test>
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445 <param name="input_format" value="wig"/>
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446 <param name="index_source" value="history"/>
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447 <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
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448 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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449 <param name="include_fails" value="False"/>
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450
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451 <output name="output" file="test_wig_01_output_a.bw"/>
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452 <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
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453 </test>
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454 <help>
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455 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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456 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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457 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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458 and VCF, reading from remote servers and file compression are supported.
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459
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460 CrossMap bed
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461 ------------
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462 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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463 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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464 </help>
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465
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466 <citations>
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467 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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468 </citations>
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469 </tool>