Mercurial > repos > mvdbeek > damidseq_core

annotate damidseq_core.xml @ 8:621837e9bfed draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 5bf4f4dbd82988d1612d951d69125bc5f5b439be
author mvdbeek
date Thu, 03 May 2018 05:12:02 -0400
parents 02f09108bcff
children
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621837e9bfed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_core commit 5bf4f4dbd82988d1612d951d69125bc5f5b439be
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1 <tool id="damidseq_core" name="damidseq" version="0.1.5">
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2 <description>align, extend and normalize a DamID-seq experiment</description>
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3 <requirements>
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4 <requirement type="package" version="1.4">damidseq_pipeline</requirement>
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5 </requirements>
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6 <version_command><![CDATA[damidseq_pipeline --help 2>&1| grep damidseq_pipeline]]></version_command>
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7 <command detect_errors="aggressive"><![CDATA[
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8 #set dam_file = 'A001.fastq.gz' if str($dam.ext).endswith('.gz') else 'A001.fastq'
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9 #set dam_fusion_file = 'A002.fastq.gz' if str($dam_fusion.ext).endswith('.gz') else 'A002.fastq'
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10 ln -f -s '$dam' $dam_file &&
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11 ln -f -s '$dam_fusion' $dam_fusion_file &&
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12 ln -f -s '$index' index.txt &&
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13 HOME="\$PWD" damidseq_pipeline
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14 --bins=$bins
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15 --bowtie=1
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16 --bowtie2_genome_dir='$reference_index.fields.path'
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17 --extend_reads=$extend_reads
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18 --extension_method='$extension_method'
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19 $full_data_files
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20 --gatc_frag_file='$gatc_frag_file'
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21 --len=$len
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22 --max_norm_value='$max_norm_value'
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23 $method_subtract
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24 --min_norm_value='$min_norm_value'
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25 --norm_method=$norm_method
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26 --norm_steps=$norm_steps
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27 --output_format=$output_format
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28 --q=$q
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29 --qscore1max=$qscore1max
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30 --qscore1min=$qscore1min
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31 --qscore2max=$qscore2max
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32 --threads=\${GALAXY_SLOTS:-4} 2>&1| LC_ALL=C sed -e 's/[^A-Za-z0-9._-]/ /g' &&
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33 #set EXT = "-ext%s" % $len if $extend_reads == '1' else ""
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34 mv 'Dam-${dam.element_identifier}${EXT}.bam' '$control_output' &&
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35 mv '${dam_fusion.element_identifier}${EXT}.bam' '$fusion_output' &&
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36 mv '${dam_fusion.element_identifier}-vs-Dam.gatc.$output_format' gatc.output
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37 #if str($full_data_files):
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38 && mv '${dam_fusion.element_identifier}-vs-Dam.$output_format' full.output
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39 #end if
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40 ]]></command>
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41 <configfiles>
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42 <configfile name="index">A1 Dam-$dam.element_identifier
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43 A2 $dam_fusion.element_identifier</configfile>
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44 </configfiles>
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45 <inputs>
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46 <param name="dam_fusion" type="data" format="fastq,fastq.gz" label="Dam fusion fastq"/>
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47 <param argument="--dam" type="data" format="fastq,fastq.gz" label="Control Dam fastq"/>
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48 <param name="reference_index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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49 <options from_data_table="bowtie2_indexes">
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50 <filter type="sort_by" column="2"/>
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51 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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52 </options>
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53 </param>
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54 <param argument="--gatc_frag_file" type="data" format="gff" label="GFF file with all GATC locations"/>
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55 <param name="output_format" type="select" label="Select the output format for the peaks">
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56 <option value="bedgraph">Bed</option>
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57 <option value="gff">GFF</option>
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58 </param>
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59 <param argument="--extend_reads" type="boolean" truevalue="1" falsevalue="0" checked="True" label="Perform read extension?"/>
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60 <param argument="--extension_method" type="select" label="Select the read extension method" help="Select Full to extend all reads or GATC to extend reads to --len or to the next GATC site, whichever is shorter. Using this option increases peak resolution (default).">
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61 <option value="gatc">To nearest GATC site</option>
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62 <option value="full">Full</option>
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63 </param>
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64 <param argument="--full_data_files" type="boolean" truevalue="--full_data_files" falsevalue="" label="Output full binned ratio files (not only GATC array)"/>
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65 <param argument="--len" type="integer" min="50" value="300" label="Length to extend reads to"/>
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66 <param argument="--bins" type="integer" min="10" value="75" label="Width of bins to use for mapping reads"/>
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67 <param argument="--min_norm_value" type="float" value="-5.0" label="Minimum log2 value to limit normalisation search at"/>
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68 <param argument="--max_norm_value" type="float" value="5.0" label="Maximum log2 value to limit normalisation search at"/>
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69 <param argument="--method_subtract" type="boolean" truevalue="--method_subtract" falsevalue="" label="Subtract Dam control values from Dam-fusion values instead of using the log2 ratio?"/>
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70 <param argument="--norm_method" type="select" label="Select normalization method">
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71 <option value="kde">kernel density estimation of log2 GATC fragment ratio (recommended)</option>
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72 <option value="rpm">readcounts per million reads (not recommended for most use cases)</option>
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73 </param>
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74 <param argument="--norm_steps" type="integer" min="1" value="300" label="Number of points in normalisation routine"/>
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75 <param argument="--q" type="integer" value="30" min="0" label="Cutoff average Q score for aligned reads"/>
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76 <param argument="--qscore1min" type="float" min="0.0" value="0.4" max="1.0" label="min decile for normalising from Dam array"/>
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77 <param argument="--qscore1max" type="float" min="0.0" value="1.0" max="1.0" label="max decile for normalising from Dam array"/>
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78 <param argument="--qscore2max" type="float" min="0.0" value="0.9" max="1.0" label="max decile for normalising from fusion-protein array"/>
0
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79 </inputs>
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80 <outputs>
8
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81 <data name="output_ratio" format="bedgraph" from_work_dir="gatc.output" label="Dam-fusion vs Dam-only GATC ratio on ${on_string}" default_identifier_source="dam_fusion">
0
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82 <change_format>
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83 <when input="output_format" value="gff" format="gff" />
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84 </change_format>
1
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85 <actions>
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86 <action type="metadata" name="dbkey">
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87 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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88 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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89 <filter type="param_value" ref="reference_index" column="0"/>
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90 </option>
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91 </action>
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92 </actions>
0
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93 </data>
8
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94 <data name="output_ratio_full" format="bedgraph" from_work_dir="full.output" label="Dam-fusion vs Dam-only full ratio on ${on_string}" default_identifier_source="dam_fusion">
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95 <filter>full_data_files</filter>
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96 <change_format>
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97 <when input="output_format" value="gff" format="gff" />
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98 </change_format>
1
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99 <actions>
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100 <action type="metadata" name="dbkey">
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101 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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102 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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103 <filter type="param_value" ref="reference_index" column="0"/>
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104 </option>
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105 </action>
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106 </actions>
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107 </data>
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108 <data name="control_output" format="bam" label="Dam-only alignment on ${on_string}" default_identifier_source="dam_fusion">
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109 <actions>
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110 <action type="metadata" name="dbkey">
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111 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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112 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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113 <filter type="param_value" ref="reference_index" column="0"/>
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114 </option>
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115 </action>
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116 </actions>
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117 </data>
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118 <data name="fusion_output" format="bam" label="Dam-fusion alignment on ${on_string}" default_identifier_source="dam_fusion">
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119 <actions>
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120 <action type="metadata" name="dbkey">
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121 <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
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122 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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123 <filter type="param_value" ref="reference_index" column="0"/>
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124 </option>
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125 </action>
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126 </actions>
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127 </data>
0
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128 </outputs>
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129 <tests>
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130 <test>
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131 <param name="dam" value="A001.fastq.gz"/>
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132 <param name="dam_fusion" value="A002.fastq.gz"/>
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133 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
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134 <param name="reference_index" value="dm6"/>
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135 <param name="norm_method" value="rpm"/>
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136 <output name="output_ratio" file="output_ratio.bed"/>
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137 <output name="control_output" file="control.bam"/>
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138 <output name="fusion_output" file="fusion.bam"/>
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139 </test>
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140 <test>
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141 <!-- test full data output -->
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142 <param name="dam" value="A001.fastq"/>
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143 <param name="dam_fusion" value="A002.fastq"/>
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144 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
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145 <param name="reference_index" value="dm6"/>
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146 <param name="norm_method" value="rpm"/>
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147 <param name="full_data_files" value="true"/>
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148 <output name="output_ratio" file="output_ratio.bed"/>
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149 <output name="output_ratio_full" file="output_ratio_full.bed"/>
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150 <output name="control_output" file="control.bam"/>
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151 <output name="fusion_output" file="fusion.bam"/>
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152 </test>
8
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153 <test>
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154 <!-- test no extension and gff outpt -->
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155 <param name="dam" value="A001.fastq"/>
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156 <param name="dam_fusion" value="A002.fastq"/>
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157 <param name="gatc_frag_file" value="dm6.GATC.gff"/>
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158 <param name="reference_index" value="dm6"/>
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159 <param name="norm_method" value="rpm"/>
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160 <param name="full_data_files" value="true"/>
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161 <param name="extend_reads" value="false"/>
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162 <param name="output_format" value="gff"/>
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163 <output name="output_ratio" file="output_ratio2.gff"/>
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164 <output name="output_ratio_full" file="output_ratio_full2.gff"/>
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165 <output name="control_output" file="control2.bam"/>
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166 <output name="fusion_output" file="fusion2.bam"/>
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167 </test>
0
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168 </tests>
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169 <help><![CDATA[
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170
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171 Processing DamID-seq data involves extending single-end reads, aligning
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172 the reads to the genome and determining the coverage, similar to
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173 processing regular ChIP-seq datasets. However, as DamID data is
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174 represented as a log2 ratio of (Dam-fusion/Dam), normalisation of the
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175 sample and Dam-only control is necessary and adding pseudocounts to
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176 mitigate the effect of background counts is highly recommended.
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177
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178 damidseq_pipeline is a single script that automatically handles
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179 sequence alignment, read extension, binned counts, normalisation,
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180 pseudocount addition and final ratio file generation. The script uses
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181 FASTQ or BAM files as input, and outputs the final log2 ratio files in
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182 bedGraph (or optionally GFF) format.
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183
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184 The output ratio files can easily be converted to TDF for viewing in IGV using
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185 igvtools. The files can be processed for peak calling using find_peaks or, if
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186 using RNA pol II DamID, transcribed genes can be determined using
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187 polii.gene.call.
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188
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189 ]]></help>
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190 <citations>
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191 <citation type="doi">10.1093/bioinformatics/btv386</citation>
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192 </citations>
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193 </tool>