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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
author wolma
date Sat, 11 Nov 2017 16:39:44 -0500
parents 85576338fbcf
children
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85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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1 <tool id="mimodd_convert" name="MiModD Convert" version="@MIMODD_WRAPPER_VERSION@">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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2 <description>converts sequence data into different formats</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <macro name="to_format">
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6 <param name="oformat" type="select" label="to">
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7 <option value="sam">sam</option>
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8 <option value="bam">bam</option>
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9 <yield />
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10 </param>
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11 </macro>
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12 <macro name="se_selector" token_format="fastq">
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13 <conditional name="input">
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14 <param name="repr" type="select"
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15 label="Single-end input data provided as">
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16 <option value="individual">Individual datasets</option>
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17 <option value="collection">Collection of datasets</option>
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18 </param>
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19 <when value="individual">
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20 <repeat name="input_data" title="fastq input datasets"
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21 default="1" min="1">
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22 <param name="file1" type="data" format="@FORMAT@"
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23 label="single-end read data"/>
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24 </repeat>
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25 </when>
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26 <when value="collection">
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27 <param name="input_data" type="data_collection"
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28 collection_type="list" format="fastq, fastq.gz"
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29 label="collection of single-end read input datasets" />
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30 </when>
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31 </conditional>
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32 <param name="header" type="data" format="sam" label="Use Header File"
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33 help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
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34
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35 </macro>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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36 <macro name="pe_selector" token_format="fastq">
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37 <conditional name="input">
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38 <param name="repr" type="select"
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39 label="Paired-end input data provided as">
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40 <option value="individual">Individual datasets</option>
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41 <option value="collection">Paired collection</option>
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42 <option value="list_of_pairs">List of pairs</option>
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43 </param>
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44 <when value="individual">
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45 <repeat name="input_data" title="fastq input datasets"
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46 default="1" min="1">
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47 <param name="file1" type="data" format="@FORMAT@"
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48 label="first set of reads of paired-end data"/>
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49 <param name="file2" type="data" format="@FORMAT@"
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50 label="second set of reads of paired-end data"/>
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51 </repeat>
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52 </when>
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53 <when value="collection">
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54 <param name="input_data" type="data_collection"
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55 collection_type="paired" format="fastq, fastq.gz"
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56 label="paired input dataset collection" />
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57 </when>
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58 <when value="list_of_pairs">
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59 <param name="input_data" type="data_collection"
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60 collection_type="list:paired" format="fastq, fastq.gz"
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61 label="nested collection of paired input datasets" />
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62 </when>
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63 </conditional>
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64 <param name="header" type="data" format="sam" label="Use Header File"
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65 help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
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66
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67 </macro>
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68 <macro name="sam_bam_selector" token_format="sam">
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69 <param name="input_data" type="data" format="@FORMAT@"
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70 label="input dataset"/>
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71 <param name="header" type="hidden" value="None"/>
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72 </macro>
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73 <macro name="fastq_output_choices">
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74 <param name="split_on_rgs" type="hidden" value=""/>
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75 <param name="reads_to_report" type="select" display="radio"
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76 label="Types of reads to generate output for"
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77 help="By default, the tool will generate two dataset collections, one for single reads found in the input file, and one for paired reads. If you know, in advance, that the input contains only single or only paired reads, you can prevent the generation of an empty dataset collection by selecting the appropriate option here.">
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78 <option value="default">Single and paired reads</option>
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79 <option value="single">Single reads only</option>
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80 <option value="paired">Paired reads only</option>
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81 </param>
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82 <param name="multisegment_report" type="boolean" checked="false"
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83 label="Generate additional output for multi-segment reads"
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84 help="Multi-segment reads, as opposed to single- and two-segment/paired reads, are not present in typical NGS data, but allowed in SAM/BAM files. If you expect multi-segment reads in the input file, enable this option." />
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85 </macro>
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86 <macro name="bam_output_choices">
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87 <param name="split_on_rgs" type="boolean" truevalue="--split-on-rgs" falsevalue="" checked="false"
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88 label="Split output based on read group IDs"
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89 help="If the input file contains reads from different read groups, write them to separate output files; implied automatically for conversions to fastq and gzipped fastq format"/>
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90 </macro>
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91 </macros>
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92 <expand macro="requirements" />
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93 <expand macro="stdio" />
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94 <expand macro="version_command" />
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95 <command><![CDATA[
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96 ## Currently Galaxy does not autoconvert collections of fastq.gz files.
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97 ## This tool wrapper fixes that by allowing fastq and fastq.gz as input
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98 ## collection formats.
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99 ## gz_input is then used as flag to indicate a fastq.gz input file
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100 #set gz_input = False
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101 #if $str($mode.output.split_on_rgs) or $str($mode.output.oformat) == "fastq" or $str($mode.output.oformat) == "gz":
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102 mkdir converted_data &&
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103 #end if
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104
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105 mimodd convert
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106 #if $str($mode.iformat) in ("sam", "bam"):
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107 '${mode.output.input_data}'
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108 #else if $str($mode.iformat) == "fastq_pe":
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109 #if $str($mode.output.input.repr) == "collection":
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110 '$mode.output.input.input_data.forward' '$mode.output.input.input_data.reverse'
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111 ## A paired collection - if the forward dataset is gzipped we assume
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112 ## the reverse dataset is too.
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113 #if $mode.output.input.input_data.forward.is_of_type('fastq.gz'):
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114 #set gz_input = True
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115 #end if
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116 #else
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117 #for $i in $mode.output.input.input_data
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118 #if $str($mode.output.input.repr) == "individual":
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119 '${i.file1}' '${i.file2}'
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120 #else
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121 '$i.forward' '$i.reverse'
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122 ## A list:paired collection - let the last forward dataset
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123 ## indicate whether input is gzipped
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124 #if $i.forward.is_of_type('fastq.gz'):
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125 #set gz_input = True
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126 #end if
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127 #end if
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128 #end for
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129 #end if
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130 #else
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131 #for $i in $mode.output.input.input_data
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132 #if $str($mode.output.input.repr) == "collection":
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133 '$i'
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134 ## A simple collection of files - the last one determines
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135 ## whether we assume gzipped input
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136 #if $i.is_of_type('fastq.gz'):
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137 #set gz_input = True
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138 #end if
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139 #else
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140 '${i.file1}'
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141 #end if
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142 #end for
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143 #end if
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144 #if $str($mode.output.header) != "None":
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145 --header '$(mode.output.header)'
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146 #end if
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147 #if $str($outputname) == "None":
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148 --ofile converted_data/read_group
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149 #else
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150 --ofile '$outputname'
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151 #end if
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152 #if $gz_input:
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153 ## a gzipped input dataset was found so lets set --iformat accordingly
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154 #if $str($mode.iformat) == "fastq_pe":
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155 --iformat gz_pe
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156 #else
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157 --iformat gz
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158 #end if
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159 #else
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160 --iformat $(mode.iformat)
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161 #end if
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162 --oformat $(mode.output.oformat)
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163 ${mode.output.split_on_rgs}
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164
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165 #if $str($mode.output.oformat) == "fastq" or $str($mode.output.oformat) == "gz":
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166 &&
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167 cd converted_data &&
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168 for f in *2segments_r1.fastq.gz; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r1.fastq.gz`_forward.fastq.gz"; done &&
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169 for f in *2segments_r2.fastq.gz; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r2.fastq.gz`_reverse.fastq.gz"; done &&
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170 for f in *2segments_r1.fastq; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r1.fastq`_forward.fastq"; done &&
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171 for f in *2segments_r2.fastq; do [ -f "\$f" ] || continue; mv "\$f" "`basename \$f _r2.fastq`_reverse.fastq"; done
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172 #end if
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173
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174 ]]></command>
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175
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176 <inputs>
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177 <conditional name="mode">
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178 <param name="iformat" type="select" label="Convert from"
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179 help="Your choice will update the interface to display further choices appropriate for your type of input data.">
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180 <option value="fastq">fastq: single-end (one file)</option>
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181 <option value="fastq_pe">fastq: paired-end (two files)</option>
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182 <option value="sam">sam</option>
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183 <option value="bam">bam</option>
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184 </param>
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185 <when value="fastq">
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186 <conditional name="output">
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187 <expand macro="to_format" />
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188 <when value="sam">
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189 <expand macro="se_selector" format="fastq" />
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190 <param name="split_on_rgs" type="hidden" value=""/>
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191 </when>
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192 <when value="bam">
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193 <expand macro="se_selector" format="fastq" />
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diff changeset
194 <param name="split_on_rgs" type="hidden" value=""/>
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diff changeset
195 </when>
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diff changeset
196 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
197 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
wolma
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diff changeset
198 <when value="fastq_pe">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
199 <conditional name="output">
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diff changeset
200 <expand macro="to_format" />
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diff changeset
201 <when value="sam">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
wolma
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diff changeset
202 <expand macro="pe_selector" format="fastq" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
203 <param name="split_on_rgs" type="hidden" value=""/>
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diff changeset
204 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
205 <when value="bam">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
206 <expand macro="pe_selector" format="fastq" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
207 <param name="split_on_rgs" type="hidden" value=""/>
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diff changeset
208 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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209 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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210 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
211 <when value="sam">
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diff changeset
212 <conditional name="output">
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diff changeset
213 <expand macro="to_format">
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diff changeset
214 <option value="fastq">fastq</option>
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215 <option value="gz">gzipped fastq</option>
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diff changeset
216 </expand>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
217 <when value="fastq">
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218 <expand macro="sam_bam_selector" format="sam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
219 <expand macro="fastq_output_choices" />
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diff changeset
220 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
221 <when value="gz">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
222 <expand macro="sam_bam_selector" format="sam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
223 <expand macro="fastq_output_choices" />
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diff changeset
224 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
225 <when value="bam">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
226 <expand macro="sam_bam_selector" format="sam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
227 <expand macro="bam_output_choices" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
228 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
229 <when value="sam">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
230 <expand macro="sam_bam_selector" format="sam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
231 <expand macro="bam_output_choices" />
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diff changeset
232 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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233 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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234 </when>
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diff changeset
235 <when value="bam">
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diff changeset
236 <conditional name="output">
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diff changeset
237 <expand macro="to_format">
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diff changeset
238 <option value="fastq">fastq</option>
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239 <option value="gz">gzipped fastq</option>
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diff changeset
240 </expand>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
241 <when value="fastq">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
242 <expand macro="sam_bam_selector" format="bam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
243 <expand macro="fastq_output_choices" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
244 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
245 <when value="gz">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
246 <expand macro="sam_bam_selector" format="bam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
247 <expand macro="fastq_output_choices" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
248 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
249 <when value="bam">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
250 <expand macro="sam_bam_selector" format="bam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
251 <expand macro="bam_output_choices" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
252 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
253 <when value="sam">
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diff changeset
254 <expand macro="sam_bam_selector" format="bam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
255 <expand macro="bam_output_choices" />
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diff changeset
256 </when>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
257 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
258 </when>
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259 </conditional>
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diff changeset
260 </inputs>
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261
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
262 <outputs>
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diff changeset
263 <data name="outputname" format="bam"
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diff changeset
264 label="Reads converted to ${mode.output.oformat} by ${tool.name} on ${on_string}">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
265 <change_format>
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diff changeset
266 <when input="mode.output.oformat" value="sam" format="sam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
267 </change_format>
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diff changeset
268 <filter>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
269 (mode['output']['oformat'] in ("bam", "sam") and not mode['output']['split_on_rgs'])
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diff changeset
270 </filter>
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diff changeset
271 </data>
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diff changeset
272 <collection name="bam_split_on_read_groups" type="list"
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diff changeset
273 label="Reads converted to ${mode.output.oformat} by ${tool.name} on ${on_string}">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
274 <discover_datasets pattern="__designation_and_ext__"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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275 directory="converted_data" />
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diff changeset
276 <filter>
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diff changeset
277 (mode['output']['oformat'] in ('bam', 'sam') and mode['output']['split_on_rgs'])
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diff changeset
278 </filter>
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diff changeset
279 </collection>
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diff changeset
280 <collection name="fastq_SE_output_split_on_read_groups" type="list"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
281 label="Single reads converted to fastq by ${tool.name} on ${on_string}">
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parents:
diff changeset
282 <discover_datasets
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diff changeset
283 pattern="(?P&lt;designation&gt;.+)_1segments_r1\.(?P&lt;ext&gt;fastq(\.gz)*)"
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diff changeset
284 directory="converted_data" />
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diff changeset
285 <filter>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
286 (mode['output']['oformat'] in ('fastq', 'gz') and mode['output']['reads_to_report'] in ('default', 'single'))
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diff changeset
287 </filter>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
288 </collection>
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diff changeset
289 <collection name="fastq_PE_reads_split_on_read_groups" type="list:paired"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
290 label="Read pairs converted to fastq by ${tool.name} on ${on_string}">
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diff changeset
291 <discover_datasets
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diff changeset
292 pattern="(?P&lt;identifier_0&gt;read_group_.+)_2segments_(?P&lt;identifier_1&gt;(forward|reverse))\.(?P&lt;ext&gt;fastq(\.gz)*)"
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293 directory="converted_data" />
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294 <filter>
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295 (mode['output']['oformat'] in ('fastq', 'gz') and mode['output']['reads_to_report'] in ('default', 'paired'))
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296 </filter>
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297 </collection>
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298 <collection name="fastq_multi-segment_reads_split_on_read_groups" type="list:list"
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299 label="Multi-segment reads converted to fastq by ${tool.name} on ${on_string}">
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300 <discover_datasets
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301 pattern="(?P&lt;identifier_0&gt;read_group_.+)_(?P&lt;identifier_1&gt;[3-9]|[1-9][0-9]+)segments_r[0-9]+\.(?P&lt;ext&gt;fastq(\.gz)*)"
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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302 directory="converted_data" />
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303 <filter>
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304 (mode['output']['oformat'] in ('fastq', 'gz') and mode['output']['multisegment_report'])
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305 </filter>
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306 </collection>
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307 </outputs>
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308
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309 <tests>
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310 <test expect_num_outputs="1">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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311 <conditional name="mode">
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312 <param name="iformat" value="fastq" />
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313 <conditional name="output">
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314 <param name="oformat" value="bam" />
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diff changeset
315 <conditional name="input">
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316 <param name="repr" value="individual" />
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diff changeset
317 <repeat name="input_data">
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318 <param name="file1"
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319 value="split_pair_reads_1.fastqsanger" />
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320 </repeat>
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321 </conditional>
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322 <param name="header" value="header_only.sam" />
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323 </conditional>
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324 </conditional>
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325 <output name="outputname" file="reads_1_w_header.bam"
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326 ftype="bam" />
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327 </test>
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328 <test expect_num_outputs="1">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
329 <conditional name="mode">
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330 <param name="iformat" value="fastq_pe" />
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diff changeset
331 <conditional name="output">
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diff changeset
332 <param name="oformat" value="bam" />
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diff changeset
333 <conditional name="input">
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diff changeset
334 <param name="repr" value="individual" />
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diff changeset
335 <repeat name="input_data">
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336 <param name="file1"
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337 value="split_pair_reads_1.fastqsanger" />
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338 <param name="file2"
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339 value="split_pair_reads_2.fastqsanger" />
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340 </repeat>
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341 </conditional>
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342 <param name="header" value="header_only.sam" />
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343 </conditional>
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344 </conditional>
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345 <output name="outputname" file="reads_1and2_w_header.bam"
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346 ftype="bam" />
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347 </test>
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348 <test expect_num_outputs="1">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
349 <conditional name="mode">
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diff changeset
350 <param name="iformat" value="fastq_pe" />
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diff changeset
351 <conditional name="output">
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diff changeset
352 <param name="oformat" value="bam" />
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diff changeset
353 <conditional name="input">
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diff changeset
354 <param name="repr" value="collection" />
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diff changeset
355 <param name="input_data">
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diff changeset
356 <collection type="paired">
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diff changeset
357 <element name="forward"
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diff changeset
358 value="split_pair_reads_1.fastqsanger" />
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diff changeset
359 <element name="reverse"
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diff changeset
360 value="split_pair_reads_2.fastqsanger" />
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diff changeset
361 </collection>
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diff changeset
362 </param>
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diff changeset
363 </conditional>
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364 <param name="header" value="header_only.sam" />
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365 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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366 </conditional>
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diff changeset
367 <output name="outputname" file="reads_1and2_w_header.bam" ftype="bam" />
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368 </test>
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diff changeset
369 <test expect_num_outputs="1">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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diff changeset
370 <conditional name="mode">
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diff changeset
371 <param name="iformat" value="bam" />
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diff changeset
372 <conditional name="output">
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diff changeset
373 <param name="oformat" value="sam" />
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diff changeset
374 <param name="input_data" value="a.bam" />
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diff changeset
375 </conditional>
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diff changeset
376 </conditional>
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diff changeset
377 <output name="outputname" file="a.sam" ftype="sam" />
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diff changeset
378 </test>
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parents:
diff changeset
379 <test>
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parents:
diff changeset
380 <conditional name="mode">
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diff changeset
381 <param name="iformat" value="sam" />
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parents:
diff changeset
382 <conditional name="output">
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parents:
diff changeset
383 <param name="oformat" value="bam" />
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parents:
diff changeset
384 <param name="input_data" value="a.sam" />
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parents:
diff changeset
385 <param name="split_on_rgs" value="true" />
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parents:
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386 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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parents:
diff changeset
387 </conditional>
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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parents:
diff changeset
388 <output_collection name="bam_split_on_read_groups" type="list" count="2">
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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parents:
diff changeset
389 <element name="read_group_000" file="a_part1.bam" ftype="bam" />
85576338fbcf planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit c4b4112ac89be8b7e43427220473269e52cb9797
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parents:
diff changeset
390 </output_collection>
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391 </test>
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392 </tests>
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393
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394 <help><![CDATA[
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395 .. class:: infomark
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396
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397 **What it does**
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398
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399 The tool converts between different file formats used for storing
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400 next-generation sequencing data.
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401
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402 As input file types it can handle fastq, SAM or BAM format, which it can
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403 convert to SAM or BAM format.
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404
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405 **Notes:**
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406
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407 1) The tool can convert fastq files representing data from paired-end
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408 sequencing runs to appropriate SAM/BAM format provided that the mate
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409 information is split over two fastq files in corresponding order.
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410
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411 **TIP:** If your paired-end data is arranged differently, you may look into
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412 the *fastq splitter* and *fastq de-interlacer* tools for Galaxy from the
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413 `Fastq Manipulation category`_ of the Galaxy Tool Shed to see if they can
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414 convert your files to the expected format.
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415
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416 2) Merging partial fastq (or gzipped fastq) files into a single SAM/BAM file is
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417 supported both for single-end and paired-end data. Simply add additional input
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418 datasets and select the appropriate files (pairs of files in case of paired-end
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419 data).
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420
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421 Concatenation of SAM/BAM file during conversion is currently not supported.
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422
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423 3) For input in fastq format a SAM header file providing run metadata
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424 **has to be specified**. The information in this file will be used as the
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425 header data of the new SAM/BAM file. You can use the *NGS Run Annotation* tool
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426 to generate a new header file for your data.
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427
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428 For input in SAM/BAM format the tool will simply copy the existing header
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429 data to the new file. To modify the header of an existing SAM/BAM file, use
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430 the *Reheader BAM file* tool instead.
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431
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432 .. _Fastq Manipulation category: https://toolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=310ff67d4caf6531
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433 .. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy
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434 .. _MiModD user guide: http://mimodd.readthedocs.org/en/latest
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435
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436 @HELP_FOOTER@
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437 ]]></help>
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438 <expand macro="citations" />
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439 </tool>