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comparison samtools_stats.xml @ 0:0d71d9467847 draft

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author devteam
date Wed, 22 Apr 2015 10:29:35 -0400
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1 <tool id="samtools_stats" name="Stats" version="2.0">
2 <description>generate statistics for BAM dataset</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"></expand>
7 <expand macro="stdio"></expand>
8 <expand macro="version_command"></expand>
9 <command><![CDATA[
10 #if $use_reference.use_ref_selector == "yes":
11 #if $use_reference.reference_source.reference_source_selector == "history":
12 ln -s "${use_reference.reference_source.ref_file}" && samtools faidx `basename "${use_reference.reference_source.ref_file}"` && samtools stats
13 #else:
14 samtools stats
15 #end if
16 #else:
17 samtools stats
18 #end if
19 "${input_file}"
20 --coverage ${coverage_min},${coverage_max},${coverage_step}
21 ${remove_dups}
22 #if str( $filter_by_flags.filter_flags ) == "filter":
23 #if $filter_by_flags.require_flags:
24 --required-flag ${sum([int(flag) for flag in str($filter_by_flags.require_flags).split(',')])}
25 #end if
26 #if $filter_by_flags.exclude_flags:
27 --filtering-flag ${sum([int(flag) for flag in str($filter_by_flags.exclude_flags).split(',')])}
28 #end if
29 #end if
30 --GC-depth ${gc_depth}
31 --insert-size ${insert_size}
32
33 ## The code below is commented out because using -I/--id options causes the following exception
34 ## Samtools-htslib: init_group_id() header parsing not yet implemented
35
36 ##if str($read_group) != "":
37 ## -I "${read_group}"
38 ##end if
39
40 #if str($read_length) != "0":
41 --read-length "${read_length}"
42 #end if
43 --most-inserts ${most_inserts}
44 --trim-quality ${trim_quality}
45 #if $use_reference.use_ref_selector == "yes":
46 #if $use_reference.reference_source.reference_source_selector != "history":
47 --ref-seq "${use_reference.reference_source.ref_file.fields.path}"
48 #else:
49 --ref-seq "${use_reference.reference_source.ref_file}"
50 #end if
51 #end if
52 > "${output}"
53 #if $split_output.split_output_selector == "yes":
54 #set outputs_to_split = str($split_output.generate_tables).split(',')
55 && mkdir split && echo ${split_output.generate_tables} &&
56
57 #if 'sn' in $outputs_to_split:
58 echo "# Summary Numbers\n" > "split/Summary numbers.tab" &&
59 grep -q ^SN "${output}" ; if [ $? = 0 ] ; then grep ^SN "${output}" | cut -f 2- >> "split/Summary numbers.tab" ; fi &&
60 #end if
61
62 #if 'ffq' in $outputs_to_split:
63 echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number\n" > "split/First Fragment Qualities.tab" &&
64 grep -q ^FFQ "${output}" ; if [ $? = 0 ] ; then grep ^FFQ "${output}" | cut -f 2- >> "split/First Fragment Qualities.tab" ; fi &&
65 #end if
66
67 #if 'lfq' in $outputs_to_split:
68 echo "# Columns correspond to qualities and rows to cycles. First column is the cycle number" > "split/Last Fragment Qualities.tab" &&
69 grep -q ^LFQ "${output}" ; if [ $? = 0 ] ; then grep ^LFQ "${output}" | cut -f 2- >> "split/Last Fragment Qualities.tab" ; fi &&
70 #end if
71
72 #if 'mpc' in $outputs_to_split:
73 echo "# Columns correspond to qualities, rows to cycles. First column is the cycle number, second is the number of N's and the rest is the number of mismatches" > "split/Mismatches per cycle.tab" &&
74 grep -q ^MPC "${output}" ; if [ $? = 0 ] ; then grep ^MPC "${output}" | cut -f 2- >> "split/Mismatches per cycle.tab" ; fi &&
75 #end if
76
77 #if 'gcf' in $outputs_to_split:
78 echo "# GC Content of first fragments" > "split/GC Content of first fragments.tab" &&
79 grep -q ^GCF "${output}" ; if [ $? = 0 ] ; then grep ^GCF "${output}" | cut -f 2- >> "split/GC Content of first fragments.tab" ; fi &&
80 #end if
81
82 #if 'gcl' in $outputs_to_split:
83 echo "# GC Content of last fragments" > "split/GC Content of last fragments.tab" &&
84 grep -q ^GCL "${output}" ; if [ $? = 0 ] ; then grep ^GCL "${output}" | cut -f 2- >> "split/GC Content of last fragments.tab" ; fi &&
85 #end if
86
87 #if 'gcc' in $outputs_to_split:
88 echo "# ACGT content per cycle. The columns are: cycle, and A,C,G,T counts (percent)" > "split/ACGT content per cycle.tab" &&
89 grep -q ^GCC "${output}" ; if [ $? = 0 ] ; then grep ^GCC "${output}" | cut -f 2- >> "split/ACGT content per cycle.tab" ; fi &&
90 #end if
91
92 #if 'is' in $outputs_to_split:
93 echo "# Insert sizes. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs" > "split/Insert sizes.tab" &&
94 grep -q ^IS "${output}" ; if [ $? = 0 ] ; then grep ^IS "${output}" | cut -f 2- >> "split/Insert sizes.tab" ; fi &&
95 #end if
96
97 #if 'rl' in $outputs_to_split:
98 echo "# Read lengths. The columns are: read length, count" > "split/Read lengths.tab" &&
99 grep -q ^RL "${output}" ; if [ $? = 0 ] ; then grep ^RL "${output}" | cut -f 2- >> "split/Read lengths.tab" ; fi &&
100 #end if
101
102 #if 'id' in $outputs_to_split:
103 echo "# Indel distribution. The columns are: length, number of insertions, number of deletions" > "split/Indel distribution.tab" &&
104 grep -q ^ID "${output}" ; if [ $? = 0 ] ; then grep ^ID "${output}" | cut -f 2- >> "split/Indel distribution.tab" ; fi &&
105 #end if
106
107 #if 'ic' in $outputs_to_split:
108 echo "# Indels per cycle. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)" > "split/Indels per cycle.tab" &&
109 grep -q ^IC "${output}" ; if [ $? = 0 ] ; then grep ^IC "${output}" | cut -f 2- >> "split/Indels per cycle.tab" ; fi &&
110 #end if
111
112 #if 'cov' in $outputs_to_split:
113 echo "# Coverage distribution" > "split/Coverage distribution.tab" &&
114 grep -q ^COV "${output}" ; if [ $? = 0 ] ; then grep ^COV "${output}" | cut -f 2- >> "split/Coverage distribution.tab" ; fi &&
115 #end if
116
117 #if 'gcd' in $outputs_to_split:
118 echo "# GC-depth. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile" > "split/GC depth.tab" &&
119 grep -q ^GCD "${output}" ; if [ $? = 0 ] ; then grep ^GCD "${output}" | cut -f 2- >> "split/GC depth.tab" ; fi &&
120 #end if
121
122 ## Unix true command below
123
124 true
125
126 #end if
127 ]]></command>
128 <inputs>
129 <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"/>
131 <param name="coverage_max" type="integer" value="1000" label="Maximum coverage" help="maximum coverage value for --coverage option"/>
132 <param name="coverage_step" type="integer" value="1" label="Coverage step" help="step value for --coverage option"/>
133 <param name="remove_dups" type="boolean" truevalue="--remove-dups" falsevalue="" checked="False" label="Exclude reads marked as duplicates" help="--remove-dups; default = False"/>
134 <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">
136 <option value="no" selected="True">a single summary file</option>
137 <option value="yes">separate datasets for each statistics</option>
138 </param>
139 <when value="no" />
140 <when value="yes">
141 <param name="generate_tables" type="select" display="checkboxes" multiple="True" label="Statistics to extract">
142 <option value="sn">Summary numbers</option>
143 <option value="ffq">First Fragment Qualities</option>
144 <option value="lfq">Last Fragment Qualities</option>
145 <option value="mpc">Mismatches per cycle</option>
146 <option value="gcf">GC Content of first fragments</option>
147 <option value="gcl">GC Content of last fragments</option>
148 <option value="gcc">ACGT content per cycle</option>
149 <option value="is">Insert sizes</option>
150 <option value="rl">Read lengths</option>
151 <option value="id">Indel distribution</option>
152 <option value="ic">Indels per cycle</option>
153 <option value="cov">Coverage distribution</option>
154 <option value="gcd">GC depth</option>
155 </param>
156 </when>
157 </conditional>
158 <conditional name="filter_by_flags">
159 <param name="filter_flags" type="select" label="Set filter by flags" help="-f and -F options">
160 <option value="nofilter" selected="True">Do not filter</option>
161 <option value="filter">Filter by flags to exclude or require</option>
162 </param>
163 <when value="filter">
164 <param name="require_flags" type="select" display="checkboxes" multiple="True" label="Require" help="-f">
165 <option value="1">Read is paired</option>
166 <option value="2">Read is mapped in a proper pair</option>
167 <option value="4">The read is unmapped</option>
168 <option value="8">The mate is unmapped</option>
169 <option value="16">Read strand</option>
170 <option value="32">Mate strand</option>
171 <option value="64">Read is the first in a pair</option>
172 <option value="128">Read is the second in a pair</option>
173 <option value="256">The alignment or this read is not primary</option>
174 <option value="512">The read fails platform/vendor quality checks</option>
175 <option value="1024">The read is a PCR or optical duplicate</option>
176 </param>
177 <param name="exclude_flags" type="select" display="checkboxes" multiple="True" label="Exclude" help="-F">
178 <option value="1">Read is paired</option>
179 <option value="2">Read is mapped in a proper pair</option>
180 <option value="4">The read is unmapped</option>
181 <option value="8">The mate is unmapped</option>
182 <option value="16">Read strand</option>
183 <option value="32">Mate strand</option>
184 <option value="64">Read is the first in a pair</option>
185 <option value="128">Read is the second in a pair</option>
186 <option value="256">The alignment or this read is not primary</option>
187 <option value="512">The read fails platform/vendor quality checks</option>
188 <option value="1024">The read is a PCR or optical duplicate</option>
189 </param>
190 </when>
191 <when value="nofilter" />
192
193 </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"/>
195 <param name="insert_size" type="integer" value="8000" label="Maximum insert size" help="--insert-size; default = 8000"/>
196
197 <!--
198
199 The -I option of samtools stats returns the following message in version 1.2:
200
201 Samtools-htslib: init_group_id() header parsing not yet implemented
202 Abort trap: 6
203
204 Because of this the section below is commented out until this stats bug is fixed
205
206 <param name="read_group" type="select" optional="true" label="Limit to a specific read group name" >
207 <options>
208 <filter type="data_meta" ref="input_file" key="read_groups" />
209 </options>
210 </param>
211
212 -->
213
214 <param name="read_length" type="integer" value="0" label="Minimum read length to generate statistics for" help="--read-length; default = no cutoff"/>
215 <param name="most_inserts" type="float" value="0.99" label="Report only the main part of inserts" help="--most-inserts; default = 0.99"/>
216 <param name="trim_quality" type="integer" value="0" label="BWA trim parameter" help="--trim-quality; default = 0"/>
217
218 <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">
220 <option value="yes">Use reference</option>
221 <option selected="True" value="no">Do not use reference</option>
222 </param>
223 <when value="yes">
224 <conditional name="reference_source">
225 <param name="reference_source_selector" type="select" label="Choose a reference sequence for GC depth">
226 <option value="cached">Locally cached</option>
227 <option value="history">History</option>
228 </param>
229 <when value="cached">
230 <param name="ref_file" type="select" label="Using genome">
231 <options from_data_table="fasta_indexes" />
232 <filter type="data_meta" ref="input_file" key="dbkey" column="1" />
233 </param>
234 </when>
235 <when value="history">
236 <param name="ref_file" type="data" format="fasta" label="Using file" />
237 </when>
238 </conditional>
239 </when>
240 <when value="no" />
241 </conditional>
242
243 </inputs>
244
245 <outputs>
246 <data format="tabular" name="output" label="${tool.name} on ${on_string}">
247 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab" ext="tabular" visible="true" directory="split" />
248 </data>
249 </outputs>
250 <tests>
251 <test>
252 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
253 <param name="use_ref_selector" value="yes" />
254 <param name="reference_source_selector" value="history" />
255 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
256 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="4" />
257 </test>
258 <test>
259 <param name="input_file" value="samtools_stats_input.bam" ftype="bam" />
260 <param name="use_ref_selector" value="yes" />
261 <param name="reference_source_selector" value="history" />
262 <param name="ref_file" value="samtools_stats_ref.fa" ftype="fasta" />
263 <param name="split_output_selector" value="yes" />
264 <param name="generate_tables" value="sn,mpc,gcc" />
265 <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" />
267 <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" />
269 </output>
270 </test>
271 </tests>
272 <help><![CDATA[
273 **What it does**
274
275 This tool runs the ``samtools stats`` command. It has the following options::
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>
294 <expand macro="citations"></expand>
295 </tool>
296