Mercurial > repos > wolma > mimodd
comparison bamsort.xml @ 23:5db0545b9004 draft
update to v0.1.7.3
author | wolma |
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date | Thu, 21 Jul 2016 03:55:49 -0400 |
parents | c46406466625 |
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22:24154c580718 | 23:5db0545b9004 |
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1 <tool id="bamsort" name="Sort BAM file" version="0.1.7.2"> | 1 <tool id="bamsort" name="Sort BAM file" version="0.1.7.3"> |
2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> | 2 <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> |
3 <macros> | 3 <macros> |
4 <import>toolshed_macros.xml</import> | 4 <import>toolshed_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements" /> |
7 <version_command>python3 -m MiModD version -q</version_command> | 7 <version_command>python3 -m MiModD version -q</version_command> |
8 <command> | 8 <command> |
9 python3 -m MiModD sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name | 9 python3 -m MiModD sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name |
10 </command> | 10 </command> |
11 | 11 |
12 <inputs> | 12 <inputs> |
13 <conditional name="input"> | 13 <conditional name="input"> |
14 <param name="iformat" type="select" label = "Input data format"> | 14 <param label="Input data format" name="iformat" type="select"> |
15 <option value="bam">bam</option> | 15 <option value="bam">bam</option> |
16 <option value="sam">sam</option> | 16 <option value="sam">sam</option> |
17 </param> | 17 </param> |
18 <when value="bam"> | 18 <when value="bam"> |
19 <param name="ifile" type="data" format="bam" label="BAM input file to sort" /> | 19 <param format="bam" label="BAM input file to sort" name="ifile" type="data" /> |
20 </when> | 20 </when> |
21 <when value="sam"> | 21 <when value="sam"> |
22 <param name="ifile" type="data" format="sam" label="SAM input file to sort" /> | 22 <param format="sam" label="SAM input file to sort" name="ifile" type="data" /> |
23 </when> | 23 </when> |
24 </conditional> | 24 </conditional> |
25 <param name="oformat" type="select" label = "Output format for the sorted data"> | 25 <param label="Output format for the sorted data" name="oformat" type="select"> |
26 <option value="bam">bam</option> | 26 <option value="bam">bam</option> |
27 <option value="sam">sam</option> | 27 <option value="sam">sam</option> |
28 </param> | 28 </param> |
29 <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." /> | 29 <param checked="false" falsevalue="" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." label="Sort by read names instead of coordinates" name="by_name" truevalue="-n" type="boolean" /> |
30 </inputs> | 30 </inputs> |
31 | 31 |
32 <outputs> | 32 <outputs> |
33 <data name="output" format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}"> | 33 <data format="bam" label="Sorted output from MiModd ${tool.name} on ${on_string}" name="output"> |
34 <change_format> | 34 <change_format> |
35 <when input="oformat" value="sam" format="sam" /> | 35 <when format="sam" input="oformat" value="sam" /> |
36 </change_format> | 36 </change_format> |
37 </data> | 37 </data> |
38 </outputs> | 38 </outputs> |
39 | 39 |
40 <help> | 40 <help> |
48 | 48 |
49 The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem. | 49 The option *Sort by read names instead of coordinates* is useful if you want to re-align coordinate-sorted paired-end data. In *paired-end mode*, the *SNAP Read Alignment* tool expects the reads in the input file to be arranged in read pairs, i.e., the forward read information of a pair must be followed immediately by its reverse mate information, which is typically not the case in coordinate-sorted files. Resorting such files by read names fixes this problem. |
50 | 50 |
51 </help> | 51 </help> |
52 </tool> | 52 </tool> |
53 |