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comparison convert.xml @ 23:5db0545b9004 draft

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update to v0.1.7.3
author wolma
date Thu, 21 Jul 2016 03:55:49 -0400
parents c46406466625
children
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22:24154c580718 23:5db0545b9004
1 <tool id="convert" name="Convert" version="0.1.7.2"> 1 <tool id="convert" name="Convert" version="0.1.7.3">
2 <description>between different sequence data formats</description> 2 <description>between different sequence data formats</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 #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz": 9 #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz":
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; 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." &gt; $output_split_on_read_groups;
11 11
12 mkdir converted_data; 12 mkdir converted_data;
13 #end if 13 #end if
14 14
15 python3 -m MiModD convert 15 python3 -m MiModD convert
34 ${mode.split_on_rgs} 34 ${mode.split_on_rgs}
35 </command> 35 </command>
36 36
37 <inputs> 37 <inputs>
38 <conditional name="mode"> 38 <conditional name="mode">
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."> 39 <param help="Your choice will update the interface to display further choices appropriate for your type of input data." label="input file format" name="iformat" type="select">
40 <option value="fastq">fastq: single-end (one file)</option> 40 <option value="fastq">fastq: single-end (one file)</option>
41 <option value="fastq_pe">fastq: paired-end (two files)</option> 41 <option value="fastq_pe">fastq: paired-end (two files)</option>
42 <option value="gz">gzip compressed fastq: single-end (one file)</option> 42 <option value="gz">gzip compressed fastq: single-end (one file)</option>
43 <option value="gz_pe">gzip compressed fastq: paired-end (two files)</option> 43 <option value="gz_pe">gzip compressed fastq: paired-end (two files)</option>
44 <option value="sam">sam</option> 44 <option value="sam">sam</option>
45 <option value="bam">bam</option> 45 <option value="bam">bam</option>
46 </param> 46 </param>
47 <when value="fastq"> 47 <when value="fastq">
48 <param name="oformat" type="select" label="output file format"> 48 <param label="output file format" name="oformat" type="select">
49 <option value="sam">sam</option> 49 <option value="sam">sam</option>
50 <option value="bam">bam</option> 50 <option value="bam">bam</option>
51 </param> 51 </param>
52 <repeat name="input_list" title="fastq input dataset" default="1" min="1"> 52 <repeat default="1" min="1" name="input_list" title="fastq input dataset">
53 <param name="file1" format="fastq" type="data" label="inputfile"/> 53 <param format="fastq" label="inputfile" name="file1" type="data" />
54 </repeat> 54 </repeat>
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."/> 55 <param format="sam" 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." label="Use Header File" name="header" type="data" />
56 <param name="split_on_rgs" type="hidden" value=""/> 56 <param name="split_on_rgs" type="hidden" value="" />
57 </when> 57 </when>
58 <when value="fastq_pe"> 58 <when value="fastq_pe">
59 <param name="oformat" type="select" label="output file format"> 59 <param label="output file format" name="oformat" type="select">
60 <option value="sam">sam</option> 60 <option value="sam">sam</option>
61 <option value="bam">bam</option> 61 <option value="bam">bam</option>
62 </param> 62 </param>
63 <repeat name="input_list" title="fastq input datasets" default="1" min="1"> 63 <repeat default="1" min="1" name="input_list" title="fastq input datasets">
64 <param format="fastq" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/> 64 <param format="fastq" label="inputfile with the first set of reads of paired-end data" name="file1" type="data" />
65 <param format="fastq" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/> 65 <param format="fastq" label="inputfile with the second set of reads of paired-end data" name="file2" type="data" />
66 </repeat> 66 </repeat>
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."/> 67 <param format="sam" 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." label="Use Header File" name="header" type="data" />
68 <param name="split_on_rgs" type="hidden" value=""/> 68 <param name="split_on_rgs" type="hidden" value="" />
69 </when> 69 </when>
70 <when value="gz"> 70 <when value="gz">
71 <param name="oformat" type="select" label="output file format"> 71 <param label="output file format" name="oformat" type="select">
72 <option value="sam">sam</option> 72 <option value="sam">sam</option>
73 <option value="bam">bam</option> 73 <option value="bam">bam</option>
74 </param> 74 </param>
75 <repeat name="input_list" title="fastq.gz input dataset" default="1" min="1"> 75 <repeat default="1" min="1" name="input_list" title="fastq.gz input dataset">
76 <param name="file1" format="data" type="data" label="inputfile"/> 76 <param format="data" label="inputfile" name="file1" type="data" />
77 </repeat> 77 </repeat>
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."/> 78 <param format="sam" 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." label="Use Header File" name="header" type="data" />
79 <param name="split_on_rgs" type="hidden" value=""/> 79 <param name="split_on_rgs" type="hidden" value="" />
80 </when> 80 </when>
81 <when value="gz_pe"> 81 <when value="gz_pe">
82 <param name="oformat" type="select" label="output file format"> 82 <param label="output file format" name="oformat" type="select">
83 <option value="sam">sam</option> 83 <option value="sam">sam</option>
84 <option value="bam">bam</option> 84 <option value="bam">bam</option>
85 </param> 85 </param>
86 <repeat name="input_list" title="fastq.gz input datasets" default="1" min="1"> 86 <repeat default="1" min="1" name="input_list" title="fastq.gz input datasets">
87 <param format="data" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/> 87 <param format="data" label="inputfile with the first set of reads of paired-end data" name="file1" type="data" />
88 <param format="data" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/> 88 <param format="data" label="inputfile with the second set of reads of paired-end data" name="file2" type="data" />
89 </repeat> 89 </repeat>
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."/> 90 <param format="sam" 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." label="Use Header File" name="header" type="data" />
91 <param name="split_on_rgs" type="hidden" value=""/> 91 <param name="split_on_rgs" type="hidden" value="" />
92 </when> 92 </when>
93 <when value="sam"> 93 <when value="sam">
94 <param name="oformat" type="select" label="output file format"> 94 <param label="output file format" name="oformat" type="select">
95 <option value="bam">bam</option> 95 <option value="bam">bam</option>
96 <option value="sam">sam</option> 96 <option value="sam">sam</option>
97 <option value="fastq">fastq</option> 97 <option value="fastq">fastq</option>
98 <option value="gz">gzipped fastq</option> 98 <option value="gz">gzipped fastq</option>
99 </param> 99 </param>
100 <repeat name="input_list" title="sam input dataset" default="1" min="1" max="1"> 100 <repeat default="1" max="1" min="1" name="input_list" title="sam input dataset">
101 <param name="file1" format="sam" type="data" label="inputfile"/> 101 <param format="sam" label="inputfile" name="file1" type="data" />
102 </repeat> 102 </repeat>
103 <param name="header" type="hidden" value="None"/> 103 <param name="header" type="hidden" value="None" />
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"/> 104 <param checked="false" falsevalue="" 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" label="Split output based on read group IDs" name="split_on_rgs" truevalue="--split-on-rgs" type="boolean" />
105 </when> 105 </when>
106 <when value="bam"> 106 <when value="bam">
107 <param name="oformat" type="select" label="output file format"> 107 <param label="output file format" name="oformat" type="select">
108 <option value="sam">sam</option> 108 <option value="sam">sam</option>
109 <option value="bam">bam</option> 109 <option value="bam">bam</option>
110 <option value="fastq">fastq</option> 110 <option value="fastq">fastq</option>
111 <option value="gz">gzipped fastq</option> 111 <option value="gz">gzipped fastq</option>
112 </param> 112 </param>
113 <repeat name="input_list" title="bam input dataset" default="1" min="1" max="1"> 113 <repeat default="1" max="1" min="1" name="input_list" title="bam input dataset">
114 <param name="file1" format="bam" type="data" label="inputfile"/> 114 <param format="bam" label="inputfile" name="file1" type="data" />
115 </repeat> 115 </repeat>
116 <param name="header" type="hidden" value="None"/> 116 <param name="header" type="hidden" value="None" />
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"/> 117 <param checked="false" falsevalue="" 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" label="Split output based on read group IDs" name="split_on_rgs" truevalue="--split-on-rgs" type="boolean" />
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 </inputs> 120 </inputs>
121 121
122 <outputs> 122 <outputs>
123 <data name="outputname" format="bam" label="Converted reads from MiModd ${tool.name} on ${on_string}"> 123 <data format="bam" label="Converted reads from MiModd ${tool.name} on ${on_string}" name="outputname">
124 <change_format> 124 <change_format>
125 <when input="mode.oformat" value="sam" format="sam" /> 125 <when format="sam" input="mode.oformat" value="sam" />
126 </change_format> 126 </change_format>
127 <filter> 127 <filter>
128 (not mode['split_on_rgs'] and mode['oformat'] not in ("fastq", "gz")) 128 (not mode['split_on_rgs'] and mode['oformat'] not in ("fastq", "gz"))
129 </filter> 129 </filter>
130 </data> 130 </data>
131 131
132 <data name="output_split_on_read_groups" format="txt" label="MiModD ${tool.name} run on ${on_string}"> 132 <data format="txt" label="MiModD ${tool.name} run on ${on_string}" name="output_split_on_read_groups">
133 <filter> 133 <filter>
134 (mode['split_on_rgs'] or mode['oformat'] in ("fastq", "gz")) 134 (mode['split_on_rgs'] or mode['oformat'] in ("fastq", "gz"))
135 </filter> 135 </filter>
136 <discover_datasets pattern="__designation_and_ext__" directory="converted_data" visible="true" /> 136 <discover_datasets directory="converted_data" pattern="__designation_and_ext__" visible="true" />
137 </data> 137 </data>
138 </outputs> 138 </outputs>
139 139
140 <help> 140 <help>
141 .. class:: infomark 141 .. class:: infomark
166 .. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy 166 .. _recipe for using gzipped fastq files in Galaxy: http://mimodd.readthedocs.org/en/latest/recipes.html#use-gzipped-fastq-files-in-galaxy
167 .. _MiModD user guide: http://mimodd.readthedocs.org/en/latest 167 .. _MiModD user guide: http://mimodd.readthedocs.org/en/latest
168 168
169 </help> 169 </help>
170 </tool> 170 </tool>
171