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comparison picard_ValidateSamFile.xml @ 7:08f69add4d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92
author devteam
date Sun, 27 Nov 2016 15:11:36 -0500
parents 52fdfc45590a
children e417b1d6288d
comparison
equal deleted inserted replaced
6:961236c5ec73 7:08f69add4d06
2 <description>assess validity of SAM/BAM dataset</description> 2 <description>assess validity of SAM/BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command> 7 <stdio>
8 8 <exit_code range="1:" level="warning"/>
9 </stdio>
10 <command><![CDATA[
11
9 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command 12 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
10 13
11 [ `ulimit -Hn` = unlimited ] &amp;&amp; ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` 14 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
12 15
13 &amp;&amp; 16 &&
14 17
15 ##set up input files 18 ##set up input files
16 19
17 #set $reference_fasta_filename = "localref.fa" 20 #set $reference_fasta_filename = "localref.fa"
18 21
19 #if str( $reference_source.reference_source_selector ) == "history": 22 #if str( $reference_source.reference_source_selector ) == "history":
20 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp; 23 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
21 #else: 24 #else:
22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 25 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
23 #end if 26 #end if
24 27
25 @java_options@ 28 @java_options@
26 29
27 java -jar \$JAVA_JAR_PATH/picard.jar 30 picard
28 ValidateSamFile 31 ValidateSamFile
29 32
30 INPUT="${inputFile}" 33 INPUT="${inputFile}"
31 OUTPUT="${outFile}" 34 OUTPUT="${outFile}"
32 MODE="${mode}" 35 MODE="${mode}"
33 36
34 #if str( $ignore ) != "None": 37 #if str( $ignore ) != "None":
35 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd 38 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
36 IGNORE="${element}" 39 IGNORE="${element}"
37 #end for 40 #end for
38 #end if 41 #end if
39 42
40 MAX_OUTPUT="${max_output}" 43 MAX_OUTPUT="${max_output}"
41 REFERENCE_SEQUENCE="${reference_fasta_filename}" 44 REFERENCE_SEQUENCE="${reference_fasta_filename}"
42 IGNORE_WARNINGS="${ignore_warnings}" 45 IGNORE_WARNINGS="${ignore_warnings}"
43 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" 46 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
44 MAX_OPEN_TEMP_FILES=`ulimit -Sn` 47 MAX_OPEN_TEMP_FILES=`ulimit -Sn`
45 48
46 VERBOSITY=ERROR 49 VERBOSITY=ERROR
47 QUIET=true 50 QUIET=true
48 51
49 </command> 52 ]]></command>
50 <inputs> 53 <inputs>
51 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." /> 54 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />
52 <conditional name="reference_source"> 55 <conditional name="reference_source">
53 <param name="reference_source_selector" type="select" label="Load reference genome from"> 56 <param name="reference_source_selector" type="select" label="Load reference genome from">
54 <option value="cached">Local cache</option> 57 <option value="cached">Local cache</option>
61 <validator type="no_options" message="No indexes are available" /> 64 <validator type="no_options" message="No indexes are available" />
62 </options> 65 </options>
63 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> 66 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
64 </param> 67 </param>
65 </when> 68 </when>
66 <when value="history"> 69 <when value="history">
67 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> 70 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />
68 </when> 71 </when>
69 </conditional> 72 </conditional>
70 73
71 <param name="mode" type="select" label="Select output mode" help="MODE"> 74 <param name="mode" type="select" label="Select output mode" help="MODE">
72 <option value="VERBOSE">Verbose</option> 75 <option value="VERBOSE">Verbose</option>
73 <option value="SUMMARY">Summary</option> 76 <option value="SUMMARY">Summary</option>
74 </param> 77 </param>
75 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE"> 78 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
133 </param> 136 </param>
134 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/> 137 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
135 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> 138 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
136 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/> 139 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
137 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/> 140 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/>
138 141
139 </inputs> 142 </inputs>
140 143
141 <outputs> 144 <outputs>
142 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/> 145 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
143 </outputs> 146 </outputs>
144 147
145 <tests> 148 <tests>
146 <test> 149 <test>
147 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/> 150 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
148 <param name="reference_source_selector" value="history"/> 151 <param name="reference_source_selector" value="history"/>
149 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/> 152 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
154 <param name="validate_index" value="True"/> 157 <param name="validate_index" value="True"/>
155 <param name="is_bisulfite_sequenced" value="False"/> 158 <param name="is_bisulfite_sequenced" value="False"/>
156 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/> 159 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
157 </test> 160 </test>
158 </tests> 161 </tests>
159 162
160 <stdio>
161 <exit_code range="1:" level="warning"/>
162 </stdio>
163
164 <help> 163 <help>
165 164
166 **Purpose** 165 **Purpose**
167 166
168 Reads a SAM/BAM dataset and report on its validity. 167 Reads a SAM/BAM dataset and report on its validity.
170 @dataset_collections@ 169 @dataset_collections@
171 170
172 @description@ 171 @description@
173 172
174 MODE=Mode 173 MODE=Mode
175 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the 174 M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the
176 default value. Possible values: {VERBOSE, SUMMARY} 175 default value. Possible values: {VERBOSE, SUMMARY}
177 176
178 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT, 177 IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT,
179 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, 178 INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED,
180 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, 179 INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR,
181 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, 180 INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND,
182 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, 181 INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT,
183 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, 182 INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR,
184 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, 183 ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX,
185 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, 184 INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START,
186 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, 185 MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER,
187 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, 186 MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER,
188 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, 187 READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN,
189 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, 188 MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE,
190 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, 189 MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE,
191 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, 190 MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH,
192 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, 191 E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE,
193 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, 192 POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED,
194 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, 193 HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE,
195 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, 194 INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE,
196 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, 195 DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE,
197 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, 196 DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END,
198 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be 197 MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be
199 specified 0 or more times. 198 specified 0 or more times.
200 199
201 MAX_OUTPUT=Integer 200 MAX_OUTPUT=Integer
202 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can 201 MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can
203 be set to 'null' to clear the default value. 202 be set to 'null' to clear the default value.
204 203
205 REFERENCE_SEQUENCE=File 204 REFERENCE_SEQUENCE=File
206 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default 205 R=File Reference sequence file, the NM tag check will be skipped if this is missing Default
207 value: null. 206 value: null.
208 207
209 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can 208 IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can
210 be set to 'null' to clear the default value. Possible values: {true, false} 209 be set to 'null' to clear the default value. Possible values: {true, false}
211 210
212 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default 211 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default
213 value: true. This option can be set to 'null' to clear the default value. Possible 212 value: true. This option can be set to 'null' to clear the default value. Possible
214 values: {true, false} 213 values: {true, false}
215 214
216 IS_BISULFITE_SEQUENCED=Boolean 215 IS_BISULFITE_SEQUENCED=Boolean
217 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not 216 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not
218 counted as an error in computing the value of the NM tag. Default value: false. This 217 counted as an error in computing the value of the NM tag. Default value: false. This
219 option can be set to 'null' to clear the default value. Possible values: {true, false} 218 option can be set to 'null' to clear the default value. Possible values: {true, false}
220 219
221 @more_info@ 220 @more_info@
222 221
223 </help> 222 </help>
224 </tool> 223 </tool>
225 224