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comparison make.sra.xml @ 0:2d09b22f4a95 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:39:51 -0400
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children 2fed4f809b76
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-1:000000000000 0:2d09b22f4a95
1 <tool profile="16.07" id="mothur_make_sra" name="Make.sra" version="@WRAPPER_VERSION@.0">
2 <description>creates the necessary files for a NCBI submission</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$project" project.dat &&
11 ln -s "$sff" sff.dat &&
12 ln -s "$oligos" oligos.dat &&
13 ln -s "$mimark" mimark.dat &&
14 ln -s "$fastq" fastq.dat &&
15
16 echo 'make.sra(
17 project=project.dat,
18 sff=sff.dat,
19 oligos=oligos.dat,
20 mimark=mimark.dat,
21 #if $fastq:
22 fastq=fastq.dat,
23 #end if
24 bdiffs=$bdiffs,
25 pdiffs=$pdiffs,
26 tdiffs=$tdiffs,
27 ldiffs=$ldiffs,
28 sdiffs=$sdiffs,
29 checkorient=$checkorient,
30 orientation=$orientation,
31 platform=$platform,
32 instrument=$instrument,
33 libstrategy=$libstrategy,
34 libselection=$libselection,
35 libsource=$libsource,
36 datatype=$datatype
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 ]]></command>
41 <inputs>
42 <param name="project" type="data" format="tabular" label="Project file"/>
43 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
44 <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>
45 <param name="mimark" type="data" format="txt" label="mimarks file - you can create the template for this file using the get.mimarkspackage command"/>
46 <param name="fastq" type="data" optional="true" format="fastq" label="fastq - provide the original fastq file"/>
47 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
48 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
49 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/>
50 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/>
51 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/>
52 <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - will check for the reverse compliment of the barcode or primer in the sequence. The default is false."/>
53 <param name="orientation" type="select" label="orientation - specify the sequence orientation">
54 <option value="forward" selected="true">forward</option>
55 <option value="reverse">reverse</option>
56 </param>
57 <param name="platform" type="select" label="platform - specify platform you are using" help="This is a controlled vocabulary section in the XML file that will be generated">
58 <option value="_LS454" selected="true">454 (_LS454)</option>
59 <option value="ILLUMINA">Illumina (ILLUMINA)</option>
60 <option value="ION_TORRENT">Ion Torrent (ION_TORRENT)</option>
61 <option value="PACBIO_SMRT">PacBio (PACBIO_SMRT)</option>
62 </param>
63 <param name="instrument" type="select" label="instrument - specify instrument" help="This is a controlled vocabulary section in the XML file that will be generated">
64 <option value="454_GS" selected="true">454_GS</option>
65 <option value="454_GS_20">454_GS_20</option>
66 <option value="454_GS_FLX">454_GS_FLX</option>
67 <option value="454_GS_FLX_Titanium">454_GS_FLX_Titanium</option>
68 <option value="454_GS_Junior">454_GS_Junior</option>
69 <option value="Illumina_Genome_Analyzer">Illumina_Genome_Analyzer</option>
70 <option value="Illumina_Genome_Analyzer_II">Illumina_Genome_Analyzer_II</option>
71 <option value="Illumina_Genome_Analyzer_IIx">Illumina_Genome_Analyzer_IIx</option>
72 <option value="Illumina_HiSeq_2000">Illumina_HiSeq_2000</option>
73 <option value="Illumina_HiSeq_1000">Illumina_HiSeq_1000</option>
74 <option value="Illumina_MiSeq">Illumina_MiSeq</option>
75 <option value="PacBio_RS">PacBio_RS</option>
76 <option value="Ion_Torrent_PGM">Ion_Torrent_PGM</option>
77 <option value="unspecified">unspecified</option>
78 </param>
79 <param name="libstrategy" type="select" label="libstrategy - specify library strategy" help="This is a controlled vocabulary section in the XML file that will be generated">
80 <option value="AMPLICON" selected="true">AMPLICON</option>
81 <option value="WGA">WGA</option>
82 <option value="WGS">WGS</option>
83 <option value="RNA-Seq">RNA-Seq</option>
84 <option value="miRNA-Se">miRNA-Se</option>
85 <option value="WCS">WCS</option>
86 <option value="CLONE">CLONE</option>
87 <option value="POOLCLONE">POOLCLONE</option>
88 <option value="CLONEEND">CLONEEND</option>
89 <option value="FINISHING">FINISHING</option>
90 <option value="ChIP-Seq">ChIP-Seq</option>
91 <option value="MNase-Seq">MNase-Seq</option>
92 <option value="DNase-Hypersensitivity">DNase-Hypersensitivity</option>
93 <option value="Bisulfite-Seq">Bisulfite-Seq</option>
94 <option value="Tn-Seq">Tn-Seq</option>
95 <option value="EST">EST</option>
96 <option value="FL-cDNA">FL-cDNA</option>
97 <option value="CTS">CTS</option>
98 <option value="MRE-Seq">MRE-Seq</option>
99 <option value="MeDIP-Seq">MeDIP-Seq</option>
100 <option value="MBD-Seq">MBD-Seq</option>
101 <option value="OTHER">OTHER</option>
102 </param>
103 <param name="libsource" type="select" label="libsource - specify library source" help="This is a controlled vocabulary section in the XML file that will be generated">
104 <option value="METAGENOMIC" selected="true">METAGENOMIC</option>
105 <option value="GENOMIC">GENOMIC</option>
106 <option value="TRANSCRIPTOMIC">TRANSCRIPTOMIC</option>
107 <option value="METATRANSCRIPTOMIC">METATRANSCRIPTOMIC</option>
108 <option value="SYNTHETIC">SYNTHETIC</option>
109 <option value="VIRAL_RNA">VIRAL_RNA</option>
110 <option value="OTHER">OTHER</option>
111 </param>
112 <param name="libselection" type="select" label="libselection - specify library selection" help="This is a controlled vocabulary section in the XML file that will be generated">
113 <option value="PCR" selected="true">PCR</option>
114 <option value="RANDOM">RANDOM</option>
115 <option value="RANDOM_PCR">RANDOM_PCR</option>
116 <option value="RT-PCR">RT-PCR</option>
117 <option value="HMPR">HMPR</option>
118 <option value="MF">MF</option>
119 <option value="CF-S">CF-S</option>
120 <option value="CF-H">CF-H</option>
121 <option value="CF-T">CF-T</option>
122 <option value="CF-M">CF-M</option>
123 <option value="MDA">MDA</option>
124 <option value="MSLL">MSLL</option>
125 <option value="cDNA">cDNA</option>
126 <option value="ChIP">ChIP</option>
127 <option value="MNase">MNase</option>
128 <option value="Hybrid_Selection">Hybrid_Selection</option>
129 <option value="Reduced_Representation">Reduced_Representation</option>
130 <option value="Restriction_Digest">Restriction_Digest</option>
131 <option value="5-methylcytidine_antibody">5-methylcytidine_antibody</option>
132 <option value="MBD2_protein_methyl-CpG_binding_domain">MBD2_protein_methyl-CpG_binding_domain</option>
133 <option value="CAGE">CAGE</option>
134 <option value="RACE">RACE</option>
135 <option value="size_fractionation">size_fractionation</option>
136 <option value="Padlock_probes_capture_method">Padlock_probes_capture_method</option>
137 <option value="other">other</option>
138 </param>
139 <param name="datatype" type="select" label="datatype - specify datatype" help="This is a controlled vocabulary section in the XML file that will be generated">
140 <option value="METAGENOME" selected="true">METAGENOME</option>
141 <option value="GENOME_SEQUENCING">GENOME_SEQUENCING</option>
142 <option value="METAGENOMIC_ASSEMBLY">METAGENOMIC_ASSEMBLY</option>
143 <option value="ASSEMBLY">ASSEMBLY</option>
144 <option value="TRANSCRIPTOME">TRANSCRIPTOME</option>
145 <option value="PROTEOMIC">PROTEOMIC</option>
146 <option value="MAP">MAP</option>
147 <option value="CLONE_ENDS">CLONE_ENDS</option>
148 <option value="TARGETED_LOCI">TARGETED_LOCI</option>
149 <option value="RANDOM_SURVEY">RANDOM_SURVEY</option>
150 <option value="EXOME">EXOME</option>
151 <option value="VARIATION">VARIATION</option>
152 <option value="EPIGENOMICS">EPIGENOMICS</option>
153 <option value="PHENOTYPE">PHENOTYPE</option>
154 <option value="GENOTYPE">GENOTYPE</option>
155 <option value="OTHER">OTHER</option>
156 </param>
157 </inputs>
158 <outputs>
159 <expand macro="logfile-output"/>
160 <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
161 <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>
162 <data name="flow_out" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flow"/>
163 <data name="scrap_sff" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap sff"/>
164 <data name="submission_xml" format="xml" from_work_dir="submission.xml" label="${tool.name} on ${on_string}: submission.xml"/>
165 </outputs>
166 <tests>
167 <test><!-- test with defauts -->
168 <param name="project" value="makesra.project" ftype="tabular"/>
169 <param name="sff" value="Fasting_Example1.sff" ftype="sff"/>
170 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
171 <param name="mimark" value="biosample.tsv" ftype="tabular"/>
172 <output name="fasta_out" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
173 <output name="qual_out" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual"/>
174 <output name="flow_out" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
175 <output name="scrap_sff" ftype="sff">
176 <assert_contents>
177 <has_text text="FLP3FBN01ELBSX"/>
178 </assert_contents>
179 </output>
180 <output name="submission_xml" ftype="xml">
181 <assert_contents>
182 <has_text text="Submission"/>
183 <has_text text="Attribute"/>
184 <has_text text="BioProject"/>
185 </assert_contents>
186 </output>
187 <expand macro="logfile-test"/>
188 </test>
189 </tests>
190 <help>
191 <![CDATA[
192
193 @MOTHUR_OVERVIEW@
194
195 **Command Documenation**
196
197 The make.sra_ creates the necessary files for a NCBI submission.
198
199 .. _make.sra: http://www.mothur.org/wiki/Make.sra
200
201 ]]>
202 </help>
203 <citations>
204 <citation type="doi">10.1128/AEM.01541-09</citation>
205 </citations>
206 </tool>