Mercurial > repos > gbcs-embl-heidelberg > je_clip
annotate je-clip.xml @ 2:b61628ae2371 draft
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
| author | gbcs-embl-heidelberg |
|---|---|
| date | Wed, 07 Dec 2016 11:57:50 -0500 |
| parents | 101525093ba1 |
| children | 2cfed59e4d27 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="je_clip" name="Je-Clip" version="1.0"> |
| 2 <description>clips Unique Molecular Identifiers (UMIs) from fastq files</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
| 8 </stdio> | |
| 9 <version_command>echo '1.0'</version_command> | |
| 10 <command interpreter="bash"> | |
| 11 <![CDATA[ | |
| 12 je clip | |
| 13 | |
| 14 ## Fastq inputs | |
| 15 @single_or_paired_cmd@ | |
| 16 #if str( $library.type ) != "single": | |
| 17 BPOS=${library.BPOS} | |
| 18 #end if | |
| 19 | |
| 20 @common_options_cmd@ | |
| 21 @barcode_len_cmd@ | |
| 22 ADD=${ADD} | |
| 23 #if str($ADD) == "false": | |
|
2
b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
24 BARCODE_RESULT_FILENAME=${BARCODE_RESULT_FILENAME} |
| 0 | 25 #end if |
| 26 | |
| 27 OF1=${OF1} | |
| 28 #if str( $library.type ) != "single": | |
| 29 OF2=${OF2} | |
| 30 #end if | |
| 31 | |
| 32 FORCE=true | |
| 33 ]]> | |
| 34 </command> | |
| 35 <inputs> | |
| 36 <!-- single/paired --> | |
| 37 <expand macro="single_or_paired_general"> | |
| 38 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes."> | |
| 39 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option> | |
| 40 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option> | |
| 41 <option value="BOTH">BOTH (beginning of both reads)</option> | |
| 42 </param> | |
| 43 </expand> | |
| 44 <expand macro="barcode_len_option"/> | |
| 45 <param name="ADD" type="boolean" | |
| 46 label="Add matched barcode at the end of the read header (ADD)" | |
| 47 truevalue="true" | |
| 48 falsevalue="false" | |
| 49 checked="true" | |
| 50 /> | |
| 51 | |
| 52 <expand macro="common_options"/> | |
| 53 | |
| 54 | |
| 55 </inputs> | |
| 56 <outputs> | |
|
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b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
57 <data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes"> |
|
b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
58 <filter>!ADD</filter> |
|
b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
59 </data> |
|
b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
60 <data name="OF1" format_source="input_1" label="Je-Clip OF1: ${on_string}"/> |
|
b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
61 <data name="OF2" format_source="input_2" label="Je-Clip OF2: ${on_string}"> |
|
b61628ae2371
planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 62411561ae3bc65ea8762d27ec79a7d912503e5b
gbcs-embl-heidelberg
parents:
0
diff
changeset
|
62 <filter>library["type"] != "single"</filter> |
| 0 | 63 </data> |
| 64 </outputs> | |
| 65 | |
| 66 <tests> | |
| 67 <test> | |
| 68 <!-- simple test on single end data --> | |
| 69 <param name="type" value="single"/> | |
| 70 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/> | |
| 71 <param name="LEN" value="6"/> | |
| 72 <param name="ADD" value="false"/> | |
| 73 <output name="BARCODE_RESULT_FILENAME" file="clip_barcode_result_file.txt"/> | |
| 74 <output name="OF1" file="clip_dataset1_SE.fastq"/> | |
| 75 </test> | |
| 76 <test> | |
| 77 <!-- more complex test on paired end data with different barcode for fwd/rev --> | |
| 78 <param name="type" value="paired"/> | |
| 79 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/> | |
| 80 <param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/> | |
| 81 <param name="LEN" value="6"/> | |
| 82 <param name="BPOS" value="BOTH"/> | |
| 83 <output name="OF1" file="clip_dataset1_PE.fastq"/> | |
| 84 <output name="OF2" file="clip_dataset2_PE.fastq"/> | |
| 85 </test> | |
| 86 </tests> | |
| 87 | |
| 88 | |
| 89 <help> | |
| 90 <![CDATA[ | |
| 91 **What it does** | |
| 92 | |
| 93 Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files | |
| 94 Input files are fastq files, and can be in gzip compressed format. | |
| 95 | |
| 96 Author: Charles Girardot (charles.girardot@embl.de). | |
| 97 | |
| 98 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de). | |
| 99 | |
| 100 ------ | |
| 101 | |
| 102 **Know what you are doing** | |
| 103 | |
| 104 .. class:: warningmark | |
| 105 | |
| 106 You will want to read the `documentation`__. | |
| 107 | |
| 108 .. __: http://gbcs.embl.de/portal/Je | |
| 109 | |
| 110 ------ | |
| 111 | |
| 112 **Parameter list** | |
| 113 | |
| 114 This is an exhaustive list of options:: | |
| 115 | |
| 116 FASTQ_FILE1=File | |
| 117 F1=File | |
| 118 | |
| 119 Input fastq file (optionally gzipped) for single end data, or first read in paired end data. | |
| 120 Required. | |
| 121 | |
| 122 FASTQ_FILE2=File | |
| 123 F2=File | |
| 124 | |
| 125 Input fastq file (optionally gzipped) for the second read of paired end data. | |
| 126 Default value: null. | |
| 127 | |
| 128 BCLEN=String | |
| 129 LEN=String | |
| 130 | |
| 131 Length of the barcode sequences. When BARCODE_READ_POS == BOTH, two distinct lengths can | |
| 132 be provided using the syntax LEN=X:Z where X and Z are 2 integers representing the | |
| 133 barcode length for read_1 and read_2 respectively. | |
| 134 Required. | |
| 135 | |
| 136 BARCODE_READ_POS=BarcodePosition | |
| 137 BPOS=BarcodePosition | |
| 138 | |
| 139 Reads containing the sequence (i.e. UMIs) to clip: | |
| 140 READ_1 (beginning of read from FASTQ_FILE_1), | |
| 141 READ_2 (beginning of read from FASTQ_FILE_2), | |
| 142 BOTH (beginning of both reads). | |
| 143 | |
| 144 Automatically set to READ_1 in single end mode and BOTH in paired end mode. Actually not | |
| 145 relevant for single end data | |
| 146 Default value: BOTH. This option can be set to 'null' to clear the default value. | |
| 147 Possible values: {READ_1, READ_2, BOTH, NONE} | |
| 148 | |
| 149 ADD_BARCODE_TO_HEADER=Boolean | |
| 150 ADD=Boolean | |
| 151 | |
| 152 Should clipped UMIs be added to the read header (at the end); apply to both barcodes when | |
| 153 BPOS=BOTH. | |
| 154 If ADD=true, the string ':barcode' is added at the end of the read header with a ':' | |
| 155 added only if current read header does not end with ':'. | |
| 156 If both reads of the pair contains a UMI (i.e. BARCODE_READ_POS == BOTH), the UMI from | |
| 157 the second read is also added to the read header. | |
| 158 Else, the header of the read without UMI receives the UMI from the other read. | |
| 159 For example: | |
| 160 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0: | |
| 161 becomes | |
| 162 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:BARCODE | |
| 163 Default value: true. This option can be set to 'null' to clear the default value. | |
| 164 Possible values: {true, false} | |
| 165 | |
| 166 ENSURE_IDENTICAL_HEADER_NAMES=Boolean | |
| 167 SAME_HEADERS=Boolean | |
| 168 | |
| 169 Makes sure headers of both reads of a pair are identical. | |
| 170 Read name (or headers) will follow the pattern (for both reads of a pair): | |
| 171 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2 | |
| 172 This option only makes sense in paired end mode and ADD=true.Some (if not all) mappers | |
| 173 will indeed complain when read headers of a read pair are not identical. | |
| 174 When SAME_HEADERS=FALSE and the RCHAR is used, read headers look like this: | |
| 175 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TGGAGTAG | |
| 176 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:CGTTGTAT | |
| 177 | |
| 178 SAME_HEADERS=true will instead generates the following identical header for both reads : | |
| 179 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TGGAGTAG:CGTTGTAT | |
| 180 Note that we also clipped the useless '1:N:0' amd '3:N:0' as they also result in | |
| 181 different headers | |
| 182 Important : this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which case | |
| 183 a space will be preserved i.e.: | |
| 184 HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT | |
| 185 | |
| 186 Default value: true. | |
| 187 This option can be set to 'null' to clear the default value. Possible values: {true, | |
| 188 false} | |
| 189 | |
| 190 READ_NAME_REPLACE_CHAR=String | |
| 191 RCHAR=String | |
| 192 | |
| 193 Replace spaces in read name/header using provided character. | |
| 194 This is needed when you need to retain ADDed barcode in read name/header during mapping | |
| 195 as everything after space in read name is usually clipped in BAM files. | |
| 196 For example, with RCHAR=':': | |
| 197 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 1:N:0: | |
| 198 becomes | |
| 199 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:1:N:0:BARCODE | |
| 200 | |
| 201 Default value: ':'. This option can be set to 'null' to clear the default value. | |
| 202 | |
| 203 XTRIMLEN=String | |
| 204 XT=String | |
| 205 | |
| 206 Optional extra number of base(s) to be trimmed right after the barcode. These extra bases | |
| 207 are not added to read headers. | |
| 208 When running paired-end, two distinct values can be given using the syntax XT=X:Z where X | |
| 209 and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when | |
| 210 BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode to | |
| 211 end up with reads of identical length (note that this can also be operated using ZT). If | |
| 212 a unique value is given, e.g. XT=1, while running paired-end the following rule applies : | |
| 213 (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode | |
| 214 (2) BPOS=BOTH, the value is used for both reads. | |
| 215 Note that XT=null is like XT=0. | |
| 216 Default value: 0. This option can be set to 'null' to clear the default value. | |
| 217 | |
| 218 ZTRIMLEN=String | |
| 219 ZT=String | |
| 220 | |
| 221 Optional extra number of bases to be trimmed from the read end i.e. 3' end. These extra | |
| 222 bases are not added to read headers. | |
| 223 When running paired-end, two distinct values can be given here using the syntax ZT=X:Z | |
| 224 where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even | |
| 225 when BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode | |
| 226 as to end up with reads of the same length (note that this can also be operated using | |
| 227 XT). Note that if a single value is passed, the value always applies to both reads in | |
| 228 paired-end mode without further consideration. | |
| 229 | |
| 230 Default value: 0. This option can be set to 'null' to clear the default value. | |
| 231 | |
| 232 BARCODE_RESULT_FILENAME=String | |
| 233 BF=String | |
| 234 | |
| 235 Optional file name where to write clipped barcodes, default name is clipped_barcodes.txt. | |
| 236 This file is automatically created if ADD=FALSE i.e. even if this option is not provided | |
| 237 by user (and always created if this option is given). | |
| 238 File format is tab delimited with: | |
| 239 ``read header (col 1) barcode from read_1 (col 2) barcode quality from read_1 (col 2)`` | |
| 240 + barcode + quality from read_2 (col 4 and 5 respectively) when relevant. | |
| 241 Can either be a name (in which case the file will be created in the output dir) or a full path. | |
| 242 Default value: null. | |
| 243 | |
| 244 ]]> | |
| 245 </help> | |
| 246 | |
| 247 </tool> |