annotate convert.xml @ 13:f0b3871cb869 draft

Uploaded
author wolma
date Mon, 25 Apr 2016 17:27:25 -0400
parents 93db2f9bca12
children c46406466625
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
93db2f9bca12 upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents: 8
diff changeset
1 <tool id="convert" name="Convert" version="0.1.7.2">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
2 <description>between different sequence data formats</description>
2
72d20758ba2c final upload
wolma
parents: 1
diff changeset
3 <macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
4 <import>toolshed_macros.xml</import>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
5 </macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
6 <expand macro="requirements"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
7 <version_command>mimodd version -q</version_command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
8 <command>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
9 #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz":
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
10 echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups;
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
11
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
12 mkdir converted_data;
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
13 #end if
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
14
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
15 mimodd convert
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
16
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17 #for $i in $mode.input_list
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
18 "${i.file1}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
19 #if $str($mode.iformat) in ("fastq_pe", "gz_pe"):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20 "${i.file2}"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
21 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
22 #end for
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 #if $str($mode.header) != "None":
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 --header "$(mode.header)"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
25 #end if
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
26
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
27 #if $str($outputname) == "None":
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
28 --ofile converted_data/read_group
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
29 #else
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
30 --ofile "$outputname"
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
31 #end if
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
32 --iformat $(mode.iformat)
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
33 --oformat $(mode.oformat)
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
34 ${mode.split_on_rgs}
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
35 </command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
36
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37 <inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 <conditional name="mode">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
39 <param name="iformat" type="select" label="input file format" help="Your choice will update the interface to display further choices appropriate for your type of input data.">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
40 <option value="fastq">fastq: single-end (one file)</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
41 <option value="fastq_pe">fastq: paired-end (two files)</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
42 <option value="gz">gzip compressed fastq: single-end (one file)</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
43 <option value="gz_pe">gzip compressed fastq: paired-end (two files)</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
44 <option value="sam">sam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
45 <option value="bam">bam</option>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
46 </param>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
47 <when value="fastq">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
48 <param name="oformat" type="select" label="output file format">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
49 <option value="sam">sam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
50 <option value="bam">bam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
51 </param>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
52 <repeat name="input_list" title="fastq input dataset" default="1" min="1">
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
53 <param name="file1" format="fastq" type="data" label="inputfile"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
54 </repeat>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
55 <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
56 <param name="split_on_rgs" type="hidden" value=""/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
57 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
58 <when value="fastq_pe">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
59 <param name="oformat" type="select" label="output file format">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
60 <option value="sam">sam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
61 <option value="bam">bam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
62 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
63 <repeat name="input_list" title="fastq input datasets" default="1" min="1">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
64 <param format="fastq" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
65 <param format="fastq" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
66 </repeat>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
67 <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
68 <param name="split_on_rgs" type="hidden" value=""/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
69 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
70 <when value="gz">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
71 <param name="oformat" type="select" label="output file format">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
72 <option value="sam">sam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
73 <option value="bam">bam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
74 </param>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
75 <repeat name="input_list" title="fastq.gz input dataset" default="1" min="1">
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
76 <param name="file1" format="data" type="data" label="inputfile"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
77 </repeat>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
78 <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
79 <param name="split_on_rgs" type="hidden" value=""/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
80 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
81 <when value="gz_pe">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
82 <param name="oformat" type="select" label="output file format">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
83 <option value="sam">sam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
84 <option value="bam">bam</option>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
85 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
86 <repeat name="input_list" title="fastq.gz input datasets" default="1" min="1">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
87 <param format="data" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
88 <param format="data" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
89 </repeat>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
90 <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
91 <param name="split_on_rgs" type="hidden" value=""/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
92 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
93 <when value="sam">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
94 <param name="oformat" type="select" label="output file format">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
95 <option value="bam">bam</option>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
96 <option value="sam">sam</option>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
97 <option value="fastq">fastq</option>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
98 <option value="gz">gzipped fastq</option>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
99 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
100 <repeat name="input_list" title="sam input dataset" default="1" min="1" max="1">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
101 <param name="file1" format="sam" type="data" label="inputfile"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
102 </repeat>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
103 <param name="header" type="hidden" value="None"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
104 <param name="split_on_rgs" type="boolean" truevalue="--split-on-rgs" falsevalue="" checked="false" label="Split output based on read group IDs" help="If the input file contains reads from different read groups, write them to separate output files; implied automatically for conversions to fastq and gzipped fastq format"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
105 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
106 <when value="bam">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
107 <param name="oformat" type="select" label="output file format">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
108 <option value="sam">sam</option>
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
109 <option value="bam">bam</option>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
110 <option value="fastq">fastq</option>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
111 <option value="gz">gzipped fastq</option>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
112 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
113 <repeat name="input_list" title="bam input dataset" default="1" min="1" max="1">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
114 <param name="file1" format="bam" type="data" label="inputfile"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
115 </repeat>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
116 <param name="header" type="hidden" value="None"/>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
117 <param name="split_on_rgs" type="boolean" truevalue="--split-on-rgs" falsevalue="" checked="false" label="Split output based on read group IDs" help="If the input file contains reads from different read groups, write them to separate output files; implied automatically for conversions to fastq and gzipped fastq format"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
118 </when>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
119 </conditional>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
120 </inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
121
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
122 <outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
123 <data name="outputname" format="bam" label="Converted reads from MiModd ${tool.name} on ${on_string}">
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
124 <change_format>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
125 <when input="mode.oformat" value="sam" format="sam" />
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
126 </change_format>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
127 <filter>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
128 (not mode['split_on_rgs'] and mode['oformat'] not in ("fastq", "gz"))
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
129 </filter>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
130 </data>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
131
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
132 <data name="output_split_on_read_groups" format="txt" label="MiModD ${tool.name} run on ${on_string}">
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
133 <filter>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
134 (mode['split_on_rgs'] or mode['oformat'] in ("fastq", "gz"))
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
135 </filter>
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
136 <discover_datasets pattern="__designation_and_ext__" directory="converted_data" visible="true" />
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
137 </data>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
138 </outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
139
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
140 <help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
141 .. class:: infomark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
142
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
143 **What it does**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
144
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
145 The tool converts between different file formats used for storing next-generation sequencing data.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
146
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
147 As input file types it can handle uncompressed or gzipped fastq, SAM or BAM format, which it can convert to SAM or BAM format.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
148
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
149 **Notes:**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
150
4
ffee8534a5c4 upgrade to mimodd version 0.1.6
Wolfgang Maier
parents: 2
diff changeset
151 1) In its standard configuration Galaxy will decompress any .gz files during their upload, so the option to convert gzipped fastq input is useful only with customized Galaxy instances or by using linked files as explained in our `recipe for using gzipped fastq files in Galaxy`_ from the `MiModD user guide`_.
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
152
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
153 2) The tool can convert fastq files representing data from paired-end sequencing runs to appropriate SAM/BAM format provided that the mate information is split over two fastq files in corresponding order.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
154
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
155 **TIP:** If your paired-end data is arranged differently, you may look into the *fastq splitter* and *fastq de-interlacer* tools for Galaxy from the `Fastq Manipulation category`_ of the Galaxy Tool Shed to see if they can convert your files to the expected format.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
156
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
157 3) Merging partial fastq (or gzipped fastq) files into a single SAM/BAM file is supported both for single-end and paired-end data. Simply add additional input datasets and select the appropriate files (pairs of files in case of paired-end data).
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
158
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
159 Concatenation of SAM/BAM file during conversion is currently not supported.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
160
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
161 4) For input in fastq format a SAM header file providing run metadata **has to be specified**. The information in this file will be used as the header data of the new SAM/BAM file. You can use the *NGS Run Annotation* tool to generate a new header file for your data.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
162
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
163 For input in SAM/BAM format the tool will simply copy the existing header data to the new file. To modify the header of an existing SAM/BAM file, use the *Reheader BAM file* tool instead.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
164
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
165 .. _Fastq Manipulation category: https://toolshed.g2.bx.psu.edu/repository/browse_repositories_in_category?id=310ff67d4caf6531
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
166 .. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
167 .. _MiModD user guide: http://mimodd.readthedocs.org/en/latest
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
168
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
169 </help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
170 </tool>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
171