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annotate samtools_stats.xml @ 2:24c5d43cb545 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:19:01 -0400
parents 0d71d9467847
children 95a7ddf617e7
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24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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1 <tool id="samtools_stats" name="Stats" version="2.0.1">
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2 <description>generate statistics for BAM dataset</description>
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3 <macros>
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4 <import>macros.xml</import>
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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5 </macros>
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6 <expand macro="requirements"/>
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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7 <expand macro="stdio"/>
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 #if $use_reference.use_ref_selector == "yes":
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11 #if $use_reference.reference_source.reference_source_selector == "history":
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12 ln -s '${use_reference.reference_source.ref_file}' &&
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 samtools faidx `basename '${use_reference.reference_source.ref_file}'` &&
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14 #end if
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15 #end if
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17 samtools stats
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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18 '${input_file}'
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19 --coverage ${coverage_min},${coverage_max},${coverage_step}
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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20 ${remove_dups}
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21
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22 #if str( $filter_by_flags.filter_flags ) == "filter":
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23 #if $filter_by_flags.require_flags:
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24 --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 #end if
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26 #if $filter_by_flags.exclude_flags:
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27 --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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28 #end if
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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29 #end if
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30
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31 --GC-depth ${gc_depth}
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32 --insert-size ${insert_size}
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33
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34 ## The code below is commented out because using -I/--id options causes the following exception
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35 ## Samtools-htslib: init_group_id() header parsing not yet implemented
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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36 ##if str($read_group) != "":
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37 ## -I "${read_group}"
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38 ##end if
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39
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40 #if str($read_length):
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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41 --read-length ${read_length}
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42 #end if
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44 --most-inserts ${most_inserts}
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45 --trim-quality ${trim_quality}
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47 #if $use_reference.use_ref_selector == "yes":
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48 #if $use_reference.reference_source.reference_source_selector != "history":
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49 --ref-seq '${use_reference.reference_source.ref_file.fields.path}'
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50 #else:
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51 --ref-seq '${use_reference.reference_source.ref_file}'
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52 #end if
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53 #end if
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54 > '${output}'
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55
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56 #if $split_output.split_output_selector == "yes":
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57 #set outputs_to_split = str($split_output.generate_tables).split(',')
2
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58 && mkdir split &&
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59 echo ${split_output.generate_tables}
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60
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61 #if 'sn' in $outputs_to_split:
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62 && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
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63 echo "" >> 'split/Summary numbers.tab' &&
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64 if grep -q ^SN '${output}'; then
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65 grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab';
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66 fi
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67 #end if
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68
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69 #if 'ffq' in $outputs_to_split:
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70 && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
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71 if grep -q ^FFQ '${output}'; then
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72 grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab';
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73 fi
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74 #end if
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75
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76 #if 'lfq' in $outputs_to_split:
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77 && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
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78 if grep -q ^LFQ '${output}'; then
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79 grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab';
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80 fi
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81 #end if
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82
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83 #if 'mpc' in $outputs_to_split:
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84 && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
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85 if grep -q ^MPC '${output}'; then
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86 grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab';
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87 fi
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88 #end if
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89
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90 #if 'gcf' in $outputs_to_split:
2
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91 && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
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92 if grep -q ^GCF '${output}'; then
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93 grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab';
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94 fi
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95 #end if
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96
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97 #if 'gcl' in $outputs_to_split:
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98 && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
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99 if grep -q ^GCL '${output}'; then
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100 grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab';
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101 fi
0
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102 #end if
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103
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104 #if 'gcc' in $outputs_to_split:
2
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105 && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
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106 if grep -q ^GCC '${output}'; then
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107 grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab';
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108 fi
0
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109 #end if
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110
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111 #if 'is' in $outputs_to_split:
2
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112 && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
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113 if grep -q ^IS '${output}'; then
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114 grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab';
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115 fi
0
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116 #end if
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117
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118 #if 'rl' in $outputs_to_split:
2
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119 && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
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120 if grep -q ^RL '${output}'; then
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121 grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab';
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122 fi
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123 #end if
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124
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125 #if 'id' in $outputs_to_split:
2
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126 && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
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127 if grep -q ^ID '${output}'; then
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128 grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab';
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129 fi
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130 #end if
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131
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132 #if 'ic' in $outputs_to_split:
2
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133 && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
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134 if grep -q ^IC '${output}'; then
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135 grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab';
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136 fi
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137 #end if
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138
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139 #if 'cov' in $outputs_to_split:
2
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140 && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
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141 if grep -q ^COV '${output}'; then
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142 grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab';
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143 fi
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144 #end if
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145
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146 #if 'gcd' in $outputs_to_split:
2
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147 && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
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148 if grep -q ^GCD '${output}'; then
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149 grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab';
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150 fi
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151 #end if
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152 #end if
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153 ]]></command>
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154 <inputs>
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155 <param name="input_file" type="data" format="sam,bam" label="BAM file" />
2
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156 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
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157 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
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158 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
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159 <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False"
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160 label="Exclude reads marked as duplicates" />
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161 <conditional name="split_output">
2
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162 <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
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163 <option value="no" selected="True">One single summary file</option>
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164 <option value="yes">Separate datasets for each statistic</option>
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165 </param>
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166 <when value="no" />
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167 <when value="yes">
2
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168 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
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169 <option value="sn">Summary numbers</option>
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170 <option value="ffq">First Fragment Qualities</option>
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171 <option value="lfq">Last Fragment Qualities</option>
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172 <option value="mpc">Mismatches per cycle</option>
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173 <option value="gcf">GC Content of first fragments</option>
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174 <option value="gcl">GC Content of last fragments</option>
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175 <option value="gcc">ACGT content per cycle</option>
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176 <option value="is">Insert sizes</option>
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177 <option value="rl">Read lengths</option>
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178 <option value="id">Indel distribution</option>
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179 <option value="ic">Indels per cycle</option>
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180 <option value="cov">Coverage distribution</option>
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181 <option value="gcd">GC depth</option>
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182 </param>
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183 </when>
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184 </conditional>
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185 <conditional name="filter_by_flags">
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186 <param name="filter_flags" type="select" label="Filter by SAM flags" help="More info on the flags: https://samtools.github.io/hts-specs/SAMv1.pdf">
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187 <option value="nofilter" selected="True">Do not filter</option>
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188 <option value="filter">Filter by flags to exclude or require</option>
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189 </param>
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190 <when value="filter">
2
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191 <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require">
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192 <option value="1">Read is paired</option>
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193 <option value="2">Read is mapped in a proper pair</option>
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194 <option value="4">The read is unmapped</option>
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195 <option value="8">The mate is unmapped</option>
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196 <option value="16">Read strand</option>
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197 <option value="32">Mate strand</option>
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198 <option value="64">Read is the first in a pair</option>
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199 <option value="128">Read is the second in a pair</option>
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200 <option value="256">The alignment or this read is not primary</option>
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201 <option value="512">The read fails platform/vendor quality checks</option>
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202 <option value="1024">The read is a PCR or optical duplicate</option>
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203 </param>
2
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204 <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude">
0
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205 <option value="1">Read is paired</option>
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206 <option value="2">Read is mapped in a proper pair</option>
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207 <option value="4">The read is unmapped</option>
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208 <option value="8">The mate is unmapped</option>
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209 <option value="16">Read strand</option>
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210 <option value="32">Mate strand</option>
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211 <option value="64">Read is the first in a pair</option>
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212 <option value="128">Read is the second in a pair</option>
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213 <option value="256">The alignment or this read is not primary</option>
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214 <option value="512">The read fails platform/vendor quality checks</option>
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215 <option value="1024">The read is a PCR or optical duplicate</option>
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216 </param>
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217 </when>
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218 <when value="nofilter" />
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219
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220 </conditional>
2
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221 <param name="gc_depth" argument="--GC-depth" type="float" value="20000" label="Size of GC-depth bins" help="Decreasing bin size increases memory requirement" />
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222 <param name="insert_size" argument="--insert-size" type="integer" value="8000" label="Maximum insert size" />
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223 <!--
0
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224
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225 The -I option of samtools stats returns the following message in version 1.2:
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226
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227 Samtools-htslib: init_group_id() header parsing not yet implemented
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228 Abort trap: 6
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229
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230 Because of this the section below is commented out until this stats bug is fixed
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231
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232 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
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233 <options>
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234 <filter type="data_meta" ref="input_file" key="read_groups" />
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235 </options>
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236 </param>
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237
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238 -->
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239
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240 <param name="read_length" argument="--read-length" type="integer" value="" optional="true" label="Minimum read length to generate statistics for" help="No cutoff if left empty"/>
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241 <param name="most_inserts" argument="--most-inserts" type="float" value="0.99" label="Report only the main part of inserts" />
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242 <param name="trim_quality" argument="--trim-quality" type="integer" value="0" label="BWA trim parameter" />
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243
0
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244 <conditional name="use_reference">
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245 <param name="use_ref_selector" argument="--ref-seq" type="select" label="Use reference sequence" help="Required for GC-depth and mismatches-per-cycle calculation">
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246 <option value="yes">Use reference</option>
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247 <option selected="True" value="no">Do not use reference</option>
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248 </param>
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249 <when value="yes">
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250 <conditional name="reference_source">
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251 <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth">
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252 <option value="cached">Locally cached</option>
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253 <option value="history">History</option>
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254 </param>
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255 <when value="cached">
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256 <param name="ref_file" type="select" label="Using genome">
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257 <options from_data_table="fasta_indexes">
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258 <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
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259 </options>
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260 </param>
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261 </when>
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262 <when value="history">
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263 <param name="ref_file" type="data" format="fasta" label="Using file" />
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264 </when>
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265 </conditional>
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266 </when>
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267 <when value="no" />
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268 </conditional>
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269
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270 </inputs>
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271
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272 <outputs>
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273 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
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274 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab" ext="tabular" visible="true" directory="split" />
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275 </data>
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276 </outputs>
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277 <tests>
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278 <test>
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279 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
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280 <param name="use_ref_selector" value="yes" />
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281 <param name="reference_source_selector" value="history" />
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282 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
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283 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
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284 </test>
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285 <test>
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286 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
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287 <param name="use_ref_selector" value="yes" />
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288 <param name="reference_source_selector" value="history" />
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289 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
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290 <param name="split_output_selector" value="yes" />
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291 <param name="generate_tables" value="sn,mpc,gcc" />
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292 <output name="output" file="samtools_stats_out2.tab" lines_diff="4">
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293 <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" />
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294 <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" />
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295 <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" />
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296 </output>
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297 </test>
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298 </tests>
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299 <help><![CDATA[
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300 **What it does**
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301
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302 This tool runs the ``samtools stats`` command.
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303 ]]></help>
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304 <expand macro="citations"/>
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305 </tool>
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306