Mercurial > repos > yhoogstrate > crossmap

annotate crossmap.xml @ 13:7e32d2a88c07 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
author yhoogstrate
date Thu, 13 Aug 2015 07:43:24 -0400
parents a5eb1023fc34
children 263581d4dd90
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1 <tool id="crossmap" name="CrossMap" version="0.2.a">
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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="0.2">crossmap</requirement>
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6 </requirements>
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8 <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
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10 <stdio>
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11 <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
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12 <regex match=".*" source="both" level="log"/>
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13 </stdio>
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15 <command>
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16 CrossMap.py
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17 ${multiple.input_format.replace("sam","bam")}
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19 #if $multiple.input_format == "vcf" and $multiple.seq_source.index_source == "cached"
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20 <!-- This is the 2nd dbkey, and the corresponding value has to be looked up -->
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21 "${filter(lambda x: str( x[1] ) == str($multiple.seq_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
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22 #else
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23 "$multiple.seq_source.input_chain"
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24 #end if
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26 #if $multiple.input_format in ["bam", "sam"]
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27 -m $multiple.insert_size
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28 -s $multiple.insert_size_stdev
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29 -t $multiple.insert_size_fold
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30 #end if
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32 "$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 #if str($multiple.include_fails) == "True"
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39 >
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40 #end if
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42 "$output"
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44 #if $multiple.input_format in ["bam", "sam"]
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45 ; mv "${output}.${multiple.input_format}" "$output"
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46 ; mv "${output}.unmap.${multiple.input_format}" "$output_unmapped"
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47 #else if $multiple.input_format in ["vcf"]
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48 ; mv "${output}" "$output"
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49 ; mv "${output}.unmap" "$output_unmapped"
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50 #end if
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51 </command>
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52
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53 <inputs>
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54 <conditional name="multiple">
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55 <param name="input_format" type="select" label="Convert a file of the following format">
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56 <option value="bam">BAM</option>
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57 <option value="sam">SAM</option>
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58 <option value="bed">BED or BED-like</option>
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59 <option value="bigwig">BigWig</option>
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60 <option value="gff">GFF or GTF</option>
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61 <option value="vcf">VCF</option>
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62 <option value="wig">Wiggle or bedGraph</option>
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63 </param>
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64 <when value="bam">
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65 <conditional name="seq_source">
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66 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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67 <option value="cached">Local data (in galaxy)</option>
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68 <option value="history">From History</option>
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69 </param>
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70 <when value="cached">
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71 <param type="data" format="bam" name="input" label="BAM/SAM file">
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72 <validator type="unspecified_build" />
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73 <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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74 </param>
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75 <param name="input_chain" type="select" label="Lift Over To">
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76 <options from_file="liftOver.loc">
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77 <column name="name" index="1"/>
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78 <column name="value" index="2"/>
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79 <column name="dbkey" index="0"/>
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80 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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81 </options>
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82 </param>
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83 </when>
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84 <when value="history">
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85 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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86 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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87 </when>
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88 </conditional>
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89
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90 <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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91 <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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92 <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]" />
13
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93
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94 <param name="include_fails" type="hidden" tvalue="False" />
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95 </when>
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96 <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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97 <conditional name="seq_source">
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98 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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99 <option value="cached">Local data (in galaxy)</option>
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100 <option value="history">From History</option>
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101 </param>
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102 <when value="cached">
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103 <param type="data" format="sam" name="input" label="BAM/SAM file">
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104 <validator type="unspecified_build" />
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105 <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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106 </param>
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107 <param name="input_chain" type="select" label="Lift Over To">
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108 <options from_file="liftOver.loc">
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109 <column name="name" index="1"/>
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110 <column name="value" index="2"/>
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111 <column name="dbkey" index="0"/>
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112 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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113 </options>
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114 </param>
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115 </when>
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116 <when value="history">
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117 <param type="data" format="bam,sam" name="input" label="BAM/SAM file" />
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118 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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119 </when>
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120 </conditional>
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121
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122 <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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123 <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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124 <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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125
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126 <param name="include_fails" type="hidden" tvalue="False" />
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127 </when>
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128 <when value="bed">
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129 <conditional name="seq_source">
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130 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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131 <option value="cached">Local data (in galaxy)</option>
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132 <option value="history">From History</option>
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133 </param>
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134 <when value="cached">
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135 <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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136 <validator type="unspecified_build" />
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137 <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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138 </param>
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139 <param name="input_chain" type="select" label="Lift Over To">
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140 <options from_file="liftOver.loc">
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141 <column name="name" index="1"/>
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142 <column name="value" index="2"/>
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143 <column name="dbkey" index="0"/>
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144 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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145 </options>
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146 </param>
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147 </when>
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148 <when value="history">
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149 <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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150 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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151 </when>
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152 </conditional>
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153
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154 <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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155 </when>
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156 <when value="bigwig">
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157 <conditional name="seq_source">
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158 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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159 <option value="cached">Local data (in galaxy)</option>
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160 <option value="history">From History</option>
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161 </param>
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162 <when value="cached">
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163 <param format="bigwig" name="input" type="data" label="BigWig file">
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164 <validator type="unspecified_build" />
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165 <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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166 </param>
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167 <param name="input_chain" type="select" label="Lift Over To">
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168 <options from_file="liftOver.loc">
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169 <column name="name" index="1"/>
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170 <column name="value" index="2"/>
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171 <column name="dbkey" index="0"/>
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172 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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173 </options>
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174 </param>
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175 </when>
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176 <when value="history">
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177 <param type="data" format="bigwig" name="input" label="BigWig file" />
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178 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
5
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179 </when>
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180 </conditional>
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181 </when>
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182 <when value="gff">
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183 <conditional name="seq_source">
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184 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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185 <option value="cached">Local data (in galaxy)</option>
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186 <option value="history">From History</option>
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187 </param>
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188 <when value="cached">
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189 <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF file">
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190 <validator type="unspecified_build" />
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191 <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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192 </param>
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193 <param name="input_chain" type="select" label="Lift Over To">
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194 <options from_file="liftOver.loc">
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195 <column name="name" index="1"/>
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196 <column name="value" index="2"/>
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197 <column name="dbkey" index="0"/>
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198 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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199 </options>
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200 </param>
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201 </when>
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202 <when value="history">
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203 <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file" />
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204 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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205 </when>
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206 </conditional>
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207
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208 <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')" />
5
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209 </when>
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210 <when value="vcf">
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211 <conditional name="seq_source">
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212 <param name="index_source" type="select" label="Source for LiftOver Data">
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213 <option value="cached">Local data (in galaxy)</option>
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214 <option value="history_chain">Chain file from History</option>
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215 <option value="history_all">Chain &amp; FASTA files from History</option>
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216 </param>
13
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217
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218 <when value="cached">
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219 <param type="data" format="vcf" name="input" label="VCF file">
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220 <validator type="unspecified_build" />
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221 <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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222 </param>
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223
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224 <!-- automatically fetch a FASTA file from the same DBKEY as the chain file -->
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225 <param name="input_chain" type="select" label="Lift Over To (Chain file)">
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226 <options from_file="liftOver.loc">
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227 <column name="name" index="1" />
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228 <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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229 <column name="dbkey" index="0" />
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230 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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231 </options>
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232 </param>
5
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233
13
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234 <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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235 <options from_file="all_fasta.loc">
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236 <column name="name" index="2"/>
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237 <column name="value" index="3"/>
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238 <column name="dbkey" index="1"/>
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239 <filter type="param_value" ref="input_chain" column="1" />
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240 </options>
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241 </param>
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242 </when>
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243
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244 <when value="history_chain">
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245 <param type="data" format="vcf" name="input" label="VCF file">
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246 <validator type="unspecified_build" />
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247 <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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248 </param>
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249 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
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250 <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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251 <options from_file="all_fasta.loc">
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252 <column name="name" index="2"/>
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253 <column name="value" index="3"/>
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254 <column name="dbkey" index="1"/>
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255 </options>
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256 </param>
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257 </when>
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258
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259 <when value="history_all">
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260 <param type="data" format="vcf" name="input" label="VCF file" />
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261 <param type="data" format="csv" name="input_chain" multiple="false" label="LiftOver chain file" />
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262 <param type="data" format="fasta" name="input_fasta" multiple="false" label="Full genome FASTA file" />
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263 </when>
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264 </conditional>
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265
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266 <param name="include_fails" type="hidden" tvalue="False" />
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267 </when>
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268 <when value="wig">
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269 <conditional name="seq_source">
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270 <param name="index_source" type="select" label="Source for LiftOver Data (chain file)">
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271 <option value="cached">Local data (in galaxy)</option>
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272 <option value="history">From History</option>
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273 </param>
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274 <when value="cached">
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275 <param format="wig" name="input" type="data" label="Wiggle file">
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276 <validator type="unspecified_build" />
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277 <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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278 </param>
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279 <param name="input_chain" type="select" label="Lift Over To">
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280 <options from_file="liftOver.loc">
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281 <column name="name" index="1"/>
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282 <column name="value" index="2"/>
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283 <column name="dbkey" index="0"/>
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284 <filter type="data_meta" ref="input" key="dbkey" column="0" />
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285 </options>
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286 </param>
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287 </when>
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288 <when value="history">
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289 <param format="wig" name="input" type="data" label="Wiggle file" />
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290 <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
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291 </when>
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292 </conditional>
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293 </when>
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294 </conditional>
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295 </inputs>
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296
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297 <outputs>
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298 <data format="text" name="output" label="${tool.name} on ">
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299 <change_format>
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300 <when input="multiple.input_format" value="bam" format="bam" />
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301 <when input="multiple.input_format" value="sam" format="sam" />
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302 <when input="multiple.input_format" value="bed" format="bed" />
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303 <when input="multiple.input_format" value="bigwig" format="bigwig" />
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304 <when input="multiple.input_format" value="gff" format="gff" />
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305 <when input="multiple.input_format" value="vcf" format="vcf" />
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306 <when input="imultiple.nput_format" value="wig" format="wig" />
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307 </change_format>
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308 </data>
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309
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310 <data format="text" name="output_unmapped" label="${tool.name} unmapped on ">
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311 <filter>input_format in ["bam" , "vcf"]</filter>
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312 <change_format>
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313 <when input="multiple.input_format" value="bam" format="bam" />
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314 <when input="multiple.input_format" value="sam" format="sam" />
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315 <when input="multiple.input_format" value="bigwig" format="bigwig" />
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316 <when input="multiple.input_format" value="gff" format="gff" />
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317 <when input="multiple.input_format" value="vcf" format="vcf" />
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318 <when input="multiple.input_format" value="wig" format="wig" />
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319 </change_format>
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320 </data>
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321 </outputs>
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322
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323 <tests>
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324 <!-- BAM/SAM -->
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325 <test>
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326 <param name="input_format" value="sam"/>
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327 <param name="index_source" value="history"/>
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328 <param name="input" value="test_bam_01_input_a.sam" ftype="sam"/>
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329 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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330 <param name="include_fails" value="False"/>
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331
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332 <output name="output" file="test_bam_01_output_a.sam" compare="diff" lines_diff="4"/>
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333 <output name="output_unmapped" file="test_bam_01_output_a.unmap.sam"/>
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334 </test>
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335
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336 <!-- BED -->
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337 <test>
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338 <param name="input_format" value="bed"/>
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339 <param name="index_source" value="history"/>
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340 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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341 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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342 <param name="include_fails" value="False"/>
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343
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344 <output name="output" file="test_bed_01_output_a__only-matches.bed"/>
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345 </test>
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346 <test>
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347 <param name="input_format" value="bed"/>
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348 <param name="index_source" value="history"/>
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349 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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350 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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351 <param name="include_fails" value="True"/>
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352
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353 <output name="output" file="test_bed_01_output_a__all.bed"/>
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354 </test>
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355 <test>
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356 <param name="input_format" value="bed"/>
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357 <param name="index_source" value="history"/>
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358 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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359 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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360 <param name="include_fails" value="False"/>
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361
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362 <output name="output" file="test_bed_02_output_a__only-matches.bed"/>
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363 </test>
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364 <test>
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365 <param name="input_format" value="bed"/>
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366 <param name="index_source" value="history"/>
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367 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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368 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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369 <param name="include_fails" value="True"/>
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370
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371 <output name="output" file="test_bed_02_output_a__all.bed"/>
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372 </test>
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373
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374 <!-- BigWig -->
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375
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376 <!-- GFF -->
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377 <test>
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378 <param name="input_format" value="gff"/>
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379 <param name="index_source" value="history"/>
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380 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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381 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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382 <param name="include_fails" value="false"/>
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383
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384 <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
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385 </test>
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386 <test>
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387 <param name="input_format" value="gff"/>
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388 <param name="index_source" value="history"/>
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389 <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
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390 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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391 <param name="include_fails" value="true"/>
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392
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393 <output name="output" file="test_gff_01_output_a__all.gtf"/>
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394 </test>
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395
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396 <!-- VCF -->
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397 <test>
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398 <param name="input_format" value="vcf"/>
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399 <param name="index_source" value="history_all"/>
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400 <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
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401 <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>
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402 <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
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403 <param name="include_fails" value="False"/>
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404
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405 <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/>
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406 <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
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407 </test>
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408
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409 <!-- WIG -->
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410 </tests>
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411
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412 <help>
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413 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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414 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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415 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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416 and VCF, reading from remote servers and file compression are supported.
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417
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418 CrossMap bed
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419 ------------
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420 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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421 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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422 </help>
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423
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424 <citations>
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425 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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426 </citations>
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427 </tool>