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comparison samtools_stats.xml @ 3:45c568e7f1f9 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 11:17:02 -0400
parents cc56fc603e53
children 8d500e0e0dbe
comparison
equal deleted inserted replaced
2:b02596e3d7a3 3:45c568e7f1f9
1 <tool id="samtools_stats" name="Stats" version="2.0"> 1 <tool id="samtools_stats" name="Stats" version="2.0.1">
2 <description>generate statistics for BAM dataset</description> 2 <description>generate statistics for BAM dataset</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #if $use_reference.use_ref_selector == "yes": 10 #if $use_reference.use_ref_selector == "yes":
11 #if $use_reference.reference_source.reference_source_selector == "history": 11 #if $use_reference.reference_source.reference_source_selector == "history":
12 ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats 12 ln -s '${use_reference.reference_source.ref_file}' &&
13 #else: 13 samtools faidx `basename '${use_reference.reference_source.ref_file}'` &&
14 samtools stats 14 #end if
15 #end if
16 #else:
17 samtools stats
18 #end if 15 #end if
19 "${input_file}" 16
20 --coverage ${coverage_min},${coverage_max},${coverage_step} 17 samtools stats
21 ${remove_dups} 18 '${input_file}'
22 #if str( $filter_by_flags.filter_flags ) == "filter": 19 --coverage ${coverage_min},${coverage_max},${coverage_step}
23 #if $filter_by_flags.require_flags: 20 ${remove_dups}
24 --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])} 21
25 #end if 22 #if str( $filter_by_flags.filter_flags ) == "filter":
26 #if $filter_by_flags.exclude_flags: 23 #if $filter_by_flags.require_flags:
27 --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])} 24 --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
28 #end if 25 #end if
29 #end if 26 #if $filter_by_flags.exclude_flags:
30 --GC-depth ${gc_depth} 27 --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
31 --insert-size ${insert_size} 28 #end if
32 29 #end if
33 ## The code below is commented out because using -I/--id options causes the following exception 30
34 ## Samtools-htslib: init_group_id() header parsing not yet implemented 31 --GC-depth ${gc_depth}
35 32 --insert-size ${insert_size}
36 ##if str($read_group) != "": 33
37 ## -I "${read_group}" 34 ## The code below is commented out because using -I/--id options causes the following exception
38 ##end if 35 ## Samtools-htslib: init_group_id() header parsing not yet implemented
39 36 ##if str($read_group) != "":
40 #if str($read_length) != "0": 37 ## -I "${read_group}"
41 --read-length "${read_length}" 38 ##end if
42 #end if 39
43 --most-inserts ${most_inserts} 40 #if str($read_length):
44 --trim-quality ${trim_quality} 41 --read-length ${read_length}
45 #if $use_reference.use_ref_selector == "yes": 42 #end if
46 #if $use_reference.reference_source.reference_source_selector != "history": 43
47 --ref-seq "${use_reference.reference_source.ref_file.fields.path}" 44 --most-inserts ${most_inserts}
48 #else: 45 --trim-quality ${trim_quality}
49 --ref-seq "${use_reference.reference_source.ref_file}" 46
50 #end if 47 #if $use_reference.use_ref_selector == "yes":
51 #end if 48 #if $use_reference.reference_source.reference_source_selector != "history":
52 > "${output}" 49 --ref-seq '${use_reference.reference_source.ref_file.fields.path}'
50 #else:
51 --ref-seq '${use_reference.reference_source.ref_file}'
52 #end if
53 #end if
54 > '${output}'
55
53 #if $split_output.split_output_selector == "yes": 56 #if $split_output.split_output_selector == "yes":
54 #set outputs_to_split = str($split_output.generate_tables).split(',') 57 #set outputs_to_split = str($split_output.generate_tables).split(',')
55 && mkdir split && echo ${split_output.generate_tables} && 58 && mkdir split &&
59 echo ${split_output.generate_tables}
56 60
57 #if 'sn' in $outputs_to_split: 61 #if 'sn' in $outputs_to_split:
58 echo "# Summary Numbers\n" > "split/Summary numbers.tab" && 62 && echo "# Summary Numbers" > 'split/Summary numbers.tab' &&
59 grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi && 63 echo "" >> 'split/Summary numbers.tab' &&
64 if grep -q ^SN '${output}'; then
65 grep ^SN '${output}' | cut -f 2- >> 'split/Summary numbers.tab';
66 fi
60 #end if 67 #end if
61 68
62 #if 'ffq' in $outputs_to_split: 69 #if 'ffq' in $outputs_to_split:
63 echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" && 70 && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > 'split/First Fragment Qualities.tab' &&
64 grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi && 71 if grep -q ^FFQ '${output}'; then
72 grep ^FFQ '${output}' | cut -f 2- >> 'split/First Fragment Qualities.tab';
73 fi
65 #end if 74 #end if
66 75
67 #if 'lfq' in $outputs_to_split: 76 #if 'lfq' in $outputs_to_split:
68 echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" && 77 && echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > 'split/Last Fragment Qualities.tab' &&
69 grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi && 78 if grep -q ^LFQ '${output}'; then
79 grep ^LFQ '${output}' | cut -f 2- >> 'split/Last Fragment Qualities.tab';
80 fi
70 #end if 81 #end if
71 82
72 #if 'mpc' in $outputs_to_split: 83 #if 'mpc' in $outputs_to_split:
73 echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" && 84 && echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > 'split/Mismatches per cycle.tab' &&
74 grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi && 85 if grep -q ^MPC '${output}'; then
86 grep ^MPC '${output}' | cut -f 2- >> 'split/Mismatches per cycle.tab';
87 fi
75 #end if 88 #end if
76 89
77 #if 'gcf' in $outputs_to_split: 90 #if 'gcf' in $outputs_to_split:
78 echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" && 91 && echo "# GC Content of first fragments" > 'split/GC Content of first fragments.tab' &&
79 grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi && 92 if grep -q ^GCF '${output}'; then
93 grep ^GCF '${output}' | cut -f 2- >> 'split/GC Content of first fragments.tab';
94 fi
80 #end if 95 #end if
81 96
82 #if 'gcl' in $outputs_to_split: 97 #if 'gcl' in $outputs_to_split:
83 echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" && 98 && echo "# GC Content of last fragments" > 'split/GC Content of last fragments.tab' &&
84 grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi && 99 if grep -q ^GCL '${output}'; then
100 grep ^GCL '${output}' | cut -f 2- >> 'split/GC Content of last fragments.tab';
101 fi
85 #end if 102 #end if
86 103
87 #if 'gcc' in $outputs_to_split: 104 #if 'gcc' in $outputs_to_split:
88 echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" && 105 && echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > 'split/ACGT content per cycle.tab' &&
89 grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi && 106 if grep -q ^GCC '${output}'; then
107 grep ^GCC '${output}' | cut -f 2- >> 'split/ACGT content per cycle.tab';
108 fi
90 #end if 109 #end if
91 110
92 #if 'is' in $outputs_to_split: 111 #if 'is' in $outputs_to_split:
93 echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" && 112 && echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > 'split/Insert sizes.tab' &&
94 grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- >> "split/Insert sizes.tab" ; fi && 113 if grep -q ^IS '${output}'; then
114 grep ^IS '${output}' | cut -f 2- >> 'split/Insert sizes.tab';
115 fi
95 #end if 116 #end if
96 117
97 #if 'rl' in $outputs_to_split: 118 #if 'rl' in $outputs_to_split:
98 echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" && 119 && echo "# Read lengths. The columns are: read length, count" > 'split/Read lengths.tab' &&
99 grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- >> "split/Read lengths.tab" ; fi && 120 if grep -q ^RL '${output}'; then
121 grep ^RL '${output}' | cut -f 2- >> 'split/Read lengths.tab';
122 fi
100 #end if 123 #end if
101 124
102 #if 'id' in $outputs_to_split: 125 #if 'id' in $outputs_to_split:
103 echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" && 126 && echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > 'split/Indel distribution.tab' &&
104 grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- >> "split/Indel distribution.tab" ; fi && 127 if grep -q ^ID '${output}'; then
128 grep ^ID '${output}' | cut -f 2- >> 'split/Indel distribution.tab';
129 fi
105 #end if 130 #end if
106 131
107 #if 'ic' in $outputs_to_split: 132 #if 'ic' in $outputs_to_split:
108 echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" && 133 && echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > 'split/Indels per cycle.tab' &&
109 grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- >> "split/Indels per cycle.tab" ; fi && 134 if grep -q ^IC '${output}'; then
135 grep ^IC '${output}' | cut -f 2- >> 'split/Indels per cycle.tab';
136 fi
110 #end if 137 #end if
111 138
112 #if 'cov' in $outputs_to_split: 139 #if 'cov' in $outputs_to_split:
113 echo "# Coverage distribution" > "split/Coverage distribution.tab" && 140 && echo "# Coverage distribution" > 'split/Coverage distribution.tab' &&
114 grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi && 141 if grep -q ^COV '${output}'; then
142 grep ^COV '${output}' | cut -f 2- >> 'split/Coverage distribution.tab';
143 fi
115 #end if 144 #end if
116 145
117 #if 'gcd' in $outputs_to_split: 146 #if 'gcd' in $outputs_to_split:
118 echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" && 147 && echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > 'split/GC depth.tab' &&
119 grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi && 148 if grep -q ^GCD '${output}'; then
120 #end if 149 grep ^GCD '${output}' | cut -f 2- >> 'split/GC depth.tab';
121 150 fi
122 ## Unix true command below 151 #end if
123
124 true
125
126 #end if 152 #end if
127 ]]></command> 153 ]]></command>
128 <inputs> 154 <inputs>
129 <param name="input_file" type="data" format="sam,bam" label="BAM file" /> 155 <param name="input_file" type="data" format="sam,bam" label="BAM file" />
130 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="minimum coverage value for --coverage option"/> 156 <param name="coverage_min" type="integer" value="1" label="Minimum coverage" help="Minimum coverage" />
131 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/> 157 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="Maximum coverage" />
132 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/> 158 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="Step value for coverage" />
133 <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/> 159 <param name="remove_dups" argument="--remove-dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False"
160 label="Exclude reads marked as duplicates" />
134 <conditional name="split_output"> 161 <conditional name="split_output">
135 <param name="split_output_selector" type="select" label="Output" help="Select between a single output or separate outputs for each statistics"> 162 <param name="split_output_selector" type="select" label="Output" help="Select between one single output or separate outputs for each statistics">
136 <option value="no" selected="True">a single summary file</option> 163 <option value="no" selected="True">One single summary file</option>
137 <option value="yes">separate datasets for each statistics</option> 164 <option value="yes">Separate datasets for each statistic</option>
138 </param> 165 </param>
139 <when value="no" /> 166 <when value="no" />
140 <when value="yes"> 167 <when value="yes">
141 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract"> 168 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Desired output files">
142 <option value="sn">Summary numbers</option> 169 <option value="sn">Summary numbers</option>
143 <option value="ffq">First Fragment Qualities</option> 170 <option value="ffq">First Fragment Qualities</option>
144 <option value="lfq">Last Fragment Qualities</option> 171 <option value="lfq">Last Fragment Qualities</option>
145 <option value="mpc">Mismatches per cycle</option> 172 <option value="mpc">Mismatches per cycle</option>
146 <option value="gcf">GC Content of first fragments</option> 173 <option value="gcf">GC Content of first fragments</option>
154 <option value="gcd">GC depth</option> 181 <option value="gcd">GC depth</option>
155 </param> 182 </param>
156 </when> 183 </when>
157 </conditional> 184 </conditional>
158 <conditional name="filter_by_flags"> 185 <conditional name="filter_by_flags">
159 <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options"> 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">
160 <option value="nofilter" selected="True">Do not filter</option> 187 <option value="nofilter" selected="True">Do not filter</option>
161 <option value="filter">Filter by flags to exclude or require</option> 188 <option value="filter">Filter by flags to exclude or require</option>
162 </param> 189 </param>
163 <when value="filter"> 190 <when value="filter">
164 <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f"> 191 <param name="require_flags" argument="-f" type="select" display="checkboxes" multiple="True" label="Require">
165 <option value="1">Read is paired</option> 192 <option value="1">Read is paired</option>
166 <option value="2">Read is mapped in a proper pair</option> 193 <option value="2">Read is mapped in a proper pair</option>
167 <option value="4">The read is unmapped</option> 194 <option value="4">The read is unmapped</option>
168 <option value="8">The mate is unmapped</option> 195 <option value="8">The mate is unmapped</option>
169 <option value="16">Read strand</option> 196 <option value="16">Read strand</option>
172 <option value="128">Read is the second in a pair</option> 199 <option value="128">Read is the second in a pair</option>
173 <option value="256">The alignment or this read is not primary</option> 200 <option value="256">The alignment or this read is not primary</option>
174 <option value="512">The read fails platform/vendor quality checks</option> 201 <option value="512">The read fails platform/vendor quality checks</option>
175 <option value="1024">The read is a PCR or optical duplicate</option> 202 <option value="1024">The read is a PCR or optical duplicate</option>
176 </param> 203 </param>
177 <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F"> 204 <param name="exclude_flags" argument="-F" type="select" display="checkboxes" multiple="True" label="Exclude">
178 <option value="1">Read is paired</option> 205 <option value="1">Read is paired</option>
179 <option value="2">Read is mapped in a proper pair</option> 206 <option value="2">Read is mapped in a proper pair</option>
180 <option value="4">The read is unmapped</option> 207 <option value="4">The read is unmapped</option>
181 <option value="8">The mate is unmapped</option> 208 <option value="8">The mate is unmapped</option>
182 <option value="16">Read strand</option> 209 <option value="16">Read strand</option>
189 </param> 216 </param>
190 </when> 217 </when>
191 <when value="nofilter" /> 218 <when value="nofilter" />
192 219
193 </conditional> 220 </conditional>
194 <param name="gc_depth" type="float" value="20000" label="GC-depth bin size" help="--GC-depth; decreasing bin size increases memory requirement; default = 20000.0"/> 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" />
195 <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/> 222 <param name="insert_size" argument="--insert-size" type="integer" value="8000" label="Maximum insert size" />
196
197 <!-- 223 <!--
198 224
199 The -I option of samtools stats returns the following message in version 1.2: 225 The -I option of samtools stats returns the following message in version 1.2:
200 226
201 Samtools-htslib: init_group_id() header parsing not yet implemented 227 Samtools-htslib: init_group_id() header parsing not yet implemented
202 Abort trap: 6 228 Abort trap: 6
203 229
204 Because of this the section below is commented out until this stats bug is fixed 230 Because of this the section below is commented out until this stats bug is fixed
205 231
206 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" > 232 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
207 <options> 233 <options>
208 <filter type="data_meta" ref="input_file" key="read_groups" /> 234 <filter type="data_meta" ref="input_file" key="read_groups" />
209 </options> 235 </options>
210 </param> 236 </param>
211 237
212 --> 238 -->
213 239
214 <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/> 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"/>
215 <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/> 241 <param name="most_inserts" argument="--most-inserts" type="float" value="0.99" label="Report only the main part of inserts" />
216 <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/> 242 <param name="trim_quality" argument="--trim-quality" type="integer" value="0" label="BWA trim parameter" />
217 243
218 <conditional name="use_reference"> 244 <conditional name="use_reference">
219 <param name="use_ref_selector" type="select" label="Use reference sequence" help="--ref-seq; required for GC-depth and mismatches-per-cycle calculation"> 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">
220 <option value="yes">Use reference</option> 246 <option value="yes">Use reference</option>
221 <option selected="True" value="no">Do not use reference</option> 247 <option selected="True" value="no">Do not use reference</option>
222 </param> 248 </param>
223 <when value="yes"> 249 <when value="yes">
224 <conditional name="reference_source"> 250 <conditional name="reference_source">
226 <option value="cached">Locally cached</option> 252 <option value="cached">Locally cached</option>
227 <option value="history">History</option> 253 <option value="history">History</option>
228 </param> 254 </param>
229 <when value="cached"> 255 <when value="cached">
230 <param name="ref_file" type="select" label="Using genome"> 256 <param name="ref_file" type="select" label="Using genome">
231 <options from_data_table="fasta_indexes" /> 257 <options from_data_table="fasta_indexes">
232 <filter type="data_meta" ref="input_file" key="dbkey" column="1" /> 258 <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
259 </options>
233 </param> 260 </param>
234 </when> 261 </when>
235 <when value="history"> 262 <when value="history">
236 <param name="ref_file" type="data" format="fasta" label="Using file" /> 263 <param name="ref_file" type="data" format="fasta" label="Using file" />
237 </when> 264 </when>
241 </conditional> 268 </conditional>
242 269
243 </inputs> 270 </inputs>
244 271
245 <outputs> 272 <outputs>
246 <data format="tabular" name="output" label="${tool.name} on ${on_string}"> 273 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
247 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab" ext="tabular" visible="true" directory="split" /> 274 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab" ext="tabular" visible="true" directory="split" />
248 </data> 275 </data>
249 </outputs> 276 </outputs>
250 <tests> 277 <tests>
251 <test> 278 <test>
261 <param name="reference_source_selector" value="history" /> 288 <param name="reference_source_selector" value="history" />
262 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" /> 289 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
263 <param name="split_output_selector" value="yes" /> 290 <param name="split_output_selector" value="yes" />
264 <param name="generate_tables" value="sn,mpc,gcc" /> 291 <param name="generate_tables" value="sn,mpc,gcc" />
265 <output name="output" file="samtools_stats_out2.tab" lines_diff="4"> 292 <output name="output" file="samtools_stats_out2.tab" lines_diff="4">
266 <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2/sn.tab" /> 293 <discovered_dataset designation="Summary numbers" ftype="tabular" file="samtools_stats_out2__sn.tab" />
267 <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2/gcc.tab" /> 294 <discovered_dataset designation="ACGT content per cycle" ftype="tabular" file="samtools_stats_out2__gcc.tab" />
268 <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2/mpc.tab" /> 295 <discovered_dataset designation="Mismatches per cycle" ftype="tabular" file="samtools_stats_out2__mpc.tab" />
269 </output> 296 </output>
270 </test> 297 </test>
271 </tests> 298 </tests>
272 <help><![CDATA[ 299 <help><![CDATA[
273 **What it does** 300 **What it does**
274 301
275 This tool runs the ``samtools stats`` command. It has the following options:: 302 This tool runs the ``samtools stats`` command.
276
277 -c, --coverage <int>,<int>,<int> Coverage distribution min,max,step [1,1000,1]
278 -d, --remove-dups Exclude from statistics reads marked as duplicates
279 -f, --required-flag <str|int> Required flag, 0 for unset. See also `samtools flags` [0]
280 -F, --filtering-flag <str|int> Filtering flag, 0 for unset. See also `samtools flags` [0]
281 --GC-depth <float> the size of GC-depth bins (decreasing bin size increases memory requirement) [2e4]
282 -h, --help This help message
283 -i, --insert-size <int> Maximum insert size [8000]
284 -I, --id <string> Include only listed read group or sample name
285 -l, --read-length <int> Include in the statistics only reads with the given read length []
286 -m, --most-inserts <float> Report only the main part of inserts [0.99]
287 -q, --trim-quality <int> The BWA trimming parameter [0]
288 -r, --ref-seq <file> Reference sequence (required for GC-depth and mismatches-per-cycle calculation). Galaxy
289 will provide options for selecting a reference cached as this Galaxy instance or choosing
290 one from history.
291
292
293 ]]></help> 303 ]]></help>
294 <expand macro="citations"></expand> 304 <expand macro="citations"/>
295 </tool> 305 </tool>
296 306