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comparison make.sra.xml @ 0:eb8c2262bd1b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:03:09 -0400
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children 82e91bb188b2
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-1:000000000000 0:eb8c2262bd1b
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$project" project.dat &&
14 ln -s "$sff" sff.dat &&
15 ln -s "$oligos" oligos.dat &&
16 ln -s "$mimark" mimark.dat &&
17 ln -s "$fastq" fastq.dat &&
18
19 echo 'make.sra(
20 project=project.dat,
21 sff=sff.dat,
22 oligos=oligos.dat,
23 mimark=mimark.dat,
24 #if $fastq:
25 fastq=fastq.dat,
26 #end if
27 bdiffs=$bdiffs,
28 pdiffs=$pdiffs,
29 tdiffs=$tdiffs,
30 ldiffs=$ldiffs,
31 sdiffs=$sdiffs,
32 checkorient=$checkorient,
33 orientation=$orientation,
34 platform=$platform,
35 instrument=$instrument,
36 libstrategy=$libstrategy,
37 libselection=$libselection,
38 libsource=$libsource,
39 datatype=$datatype
40 )'
41 | sed 's/ //g' ## mothur trips over whitespace
42 | mothur
43 | tee mothur.out.log
44 ]]></command>
45 <inputs>
46 <param name="project" type="data" format="tabular" label="Project file"/>
47 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
48 <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"/>
49 <param name="mimark" type="data" format="txt" label="mimarks file - you can create the template for this file using the get.mimarkspackage command"/>
50 <param name="fastq" type="data" optional="true" format="fastq" label="fastq - provide the original fastq file"/>
51 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
52 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
53 <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)"/>
54 <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)"/>
55 <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)"/>
56 <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."/>
57 <param name="orientation" type="select" label="orientation - specify the sequence orientation">
58 <option value="forward" selected="true">forward</option>
59 <option value="reverse">reverse</option>
60 </param>
61 <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">
62 <option value="_LS454" selected="true">454 (_LS454)</option>
63 <option value="ILLUMINA">Illumina (ILLUMINA)</option>
64 <option value="ION_TORRENT">Ion Torrent (ION_TORRENT)</option>
65 <option value="PACBIO_SMRT">PacBio (PACBIO_SMRT)</option>
66 </param>
67 <param name="instrument" type="select" label="instrument - specify instrument" help="This is a controlled vocabulary section in the XML file that will be generated">
68 <option value="454_GS" selected="true">454_GS</option>
69 <option value="454_GS_20">454_GS_20</option>
70 <option value="454_GS_FLX">454_GS_FLX</option>
71 <option value="454_GS_FLX_Titanium">454_GS_FLX_Titanium</option>
72 <option value="454_GS_Junior">454_GS_Junior</option>
73 <option value="Illumina_Genome_Analyzer">Illumina_Genome_Analyzer</option>
74 <option value="Illumina_Genome_Analyzer_II">Illumina_Genome_Analyzer_II</option>
75 <option value="Illumina_Genome_Analyzer_IIx">Illumina_Genome_Analyzer_IIx</option>
76 <option value="Illumina_HiSeq_2000">Illumina_HiSeq_2000</option>
77 <option value="Illumina_HiSeq_1000">Illumina_HiSeq_1000</option>
78 <option value="Illumina_MiSeq">Illumina_MiSeq</option>
79 <option value="PacBio_RS">PacBio_RS</option>
80 <option value="Ion_Torrent_PGM">Ion_Torrent_PGM</option>
81 <option value="unspecified">unspecified</option>
82 </param>
83 <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">
84 <option value="AMPLICON" selected="true">AMPLICON</option>
85 <option value="WGA">WGA</option>
86 <option value="WGS">WGS</option>
87 <option value="RNA-Seq">RNA-Seq</option>
88 <option value="miRNA-Se">miRNA-Se</option>
89 <option value="WCS">WCS</option>
90 <option value="CLONE">CLONE</option>
91 <option value="POOLCLONE">POOLCLONE</option>
92 <option value="CLONEEND">CLONEEND</option>
93 <option value="FINISHING">FINISHING</option>
94 <option value="ChIP-Seq">ChIP-Seq</option>
95 <option value="MNase-Seq">MNase-Seq</option>
96 <option value="DNase-Hypersensitivity">DNase-Hypersensitivity</option>
97 <option value="Bisulfite-Seq">Bisulfite-Seq</option>
98 <option value="Tn-Seq">Tn-Seq</option>
99 <option value="EST">EST</option>
100 <option value="FL-cDNA">FL-cDNA</option>
101 <option value="CTS">CTS</option>
102 <option value="MRE-Seq">MRE-Seq</option>
103 <option value="MeDIP-Seq">MeDIP-Seq</option>
104 <option value="MBD-Seq">MBD-Seq</option>
105 <option value="OTHER">OTHER</option>
106 </param>
107 <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">
108 <option value="METAGENOMIC" selected="true">METAGENOMIC</option>
109 <option value="GENOMIC">GENOMIC</option>
110 <option value="TRANSCRIPTOMIC">TRANSCRIPTOMIC</option>
111 <option value="METATRANSCRIPTOMIC">METATRANSCRIPTOMIC</option>
112 <option value="SYNTHETIC">SYNTHETIC</option>
113 <option value="VIRAL_RNA">VIRAL_RNA</option>
114 <option value="OTHER">OTHER</option>
115 </param>
116 <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">
117 <option value="PCR" selected="true">PCR</option>
118 <option value="RANDOM">RANDOM</option>
119 <option value="RANDOM_PCR">RANDOM_PCR</option>
120 <option value="RT-PCR">RT-PCR</option>
121 <option value="HMPR">HMPR</option>
122 <option value="MF">MF</option>
123 <option value="CF-S">CF-S</option>
124 <option value="CF-H">CF-H</option>
125 <option value="CF-T">CF-T</option>
126 <option value="CF-M">CF-M</option>
127 <option value="MDA">MDA</option>
128 <option value="MSLL">MSLL</option>
129 <option value="cDNA">cDNA</option>
130 <option value="ChIP">ChIP</option>
131 <option value="MNase">MNase</option>
132 <option value="Hybrid_Selection">Hybrid_Selection</option>
133 <option value="Reduced_Representation">Reduced_Representation</option>
134 <option value="Restriction_Digest">Restriction_Digest</option>
135 <option value="5-methylcytidine_antibody">5-methylcytidine_antibody</option>
136 <option value="MBD2_protein_methyl-CpG_binding_domain">MBD2_protein_methyl-CpG_binding_domain</option>
137 <option value="CAGE">CAGE</option>
138 <option value="RACE">RACE</option>
139 <option value="size_fractionation">size_fractionation</option>
140 <option value="Padlock_probes_capture_method">Padlock_probes_capture_method</option>
141 <option value="other">other</option>
142 </param>
143 <param name="datatype" type="select" label="datatype - specify datatype" help="This is a controlled vocabulary section in the XML file that will be generated">
144 <option value="METAGENOME" selected="true">METAGENOME</option>
145 <option value="GENOME_SEQUENCING">GENOME_SEQUENCING</option>
146 <option value="METAGENOMIC_ASSEMBLY">METAGENOMIC_ASSEMBLY</option>
147 <option value="ASSEMBLY">ASSEMBLY</option>
148 <option value="TRANSCRIPTOME">TRANSCRIPTOME</option>
149 <option value="PROTEOMIC">PROTEOMIC</option>
150 <option value="MAP">MAP</option>
151 <option value="CLONE_ENDS">CLONE_ENDS</option>
152 <option value="TARGETED_LOCI">TARGETED_LOCI</option>
153 <option value="RANDOM_SURVEY">RANDOM_SURVEY</option>
154 <option value="EXOME">EXOME</option>
155 <option value="VARIATION">VARIATION</option>
156 <option value="EPIGENOMICS">EPIGENOMICS</option>
157 <option value="PHENOTYPE">PHENOTYPE</option>
158 <option value="GENOTYPE">GENOTYPE</option>
159 <option value="OTHER">OTHER</option>
160 </param>
161 </inputs>
162 <outputs>
163 <expand macro="logfile-output"/>
164 <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
165 <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>
166 <data name="flow_out" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flow"/>
167 <data name="scrap_sff" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap sff"/>
168 <data name="submission_xml" format="xml" from_work_dir="submission.xml" label="${tool.name} on ${on_string}: submission.xml"/>
169 </outputs>
170 <tests>
171 <test><!-- test with defauts -->
172 <param name="project" value="makesra.project" ftype="tabular"/>
173 <param name="sff" value="Fasting_Example1.sff" ftype="sff"/>
174 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
175 <param name="mimark" value="biosample.tsv" ftype="tabular"/>
176 <output name="fasta_out" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
177 <output name="qual_out" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual"/>
178 <output name="flow_out" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
179 <output name="scrap_sff" ftype="sff">
180 <assert_contents>
181 <has_text text="FLP3FBN01ELBSX"/>
182 </assert_contents>
183 </output>
184 <output name="submission_xml" ftype="xml">
185 <assert_contents>
186 <has_text text="Submission"/>
187 <has_text text="Attribute"/>
188 <has_text text="BioProject"/>
189 </assert_contents>
190 </output>
191 <expand macro="logfile-test"/>
192 </test>
193 </tests>
194 <help>
195 <![CDATA[
196
197 @MOTHUR_OVERVIEW@
198
199 **Command Documentation**
200
201 The make.sra_ creates the necessary files for a NCBI submission.
202
203 .. _make.sra: https://www.mothur.org/wiki/Make.sra
204
205 ]]>
206 </help>
207 <citations>
208 <citation type="doi">10.1128/AEM.01541-09</citation>
209 </citations>
210 </tool>