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comparison slamdunk.xml @ 1:57bf9a0d49a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
author iuc
date Sun, 20 Jan 2019 06:51:15 -0500
parents 3fd7458bc861
children fae4a5ec0653
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0:3fd7458bc861 1:57bf9a0d49a5
1 <tool id="slamdunk" name="Slamdunk" version="0.3.3"> 1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1">
2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description> 2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="0.3.3">slamdunk</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements" />
6 <version_command>slamdunk --version</version_command> 7 <version_command>slamdunk --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
8 #if $reference_source.reference_source_selector == 'history': 9 #if $reference_source.reference_source_selector == 'history':
9 ln -f -s '$reference_source.ref_file' reference.fa && 10 ln -f -s '$reference_source.ref_file' reference.fa &&
10 #else: 11 #else:
28 -rl $readLength 29 -rl $readLength
29 -c $covThresh 30 -c $covThresh
30 '$Reads' 31 '$Reads'
31 ]]></command> 32 ]]></command>
32 <inputs> 33 <inputs>
33 <conditional name="reference_source"> 34 <expand macro="reference_files" />
34 <param name="reference_source_selector" type="select" label="Genome" help="Select a built-in FASTA file (if available) or one from the history"> 35 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/>
35 <option value="cached">Use a built-in FASTA</option>
36 <option value="history">Use a FASTA from history</option>
37 </param>
38 <when value="cached">
39 <param name="ref_file" type="select" label="Use built-in FASTA" help="Select genome from the list">
40 <options from_data_table="all_fasta">
41 <filter type="sort_by" column="2" />
42 <validator type="no_options" message="No reference genomes are available" />
43 </options>
44 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
45 </param>
46 </when>
47 <when value="history">
48 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the FASTA" help="You can upload a FASTA sequence to the history and use it as reference" />
49 </when>
50 </conditional>
51 <param name="Reference" type="data" format="bed" />
52 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" />
53 <section name="multimapper" title="Multimapper recovery" 36 <section name="multimapper" title="Multimapper recovery"
54 expanded="false"> 37 expanded="false">
55 <section name="filterbed" 38 <section name="filterbed"
56 title="Use separate 3' UTR bed to filter multimappers." expanded="false"> 39 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
57 <param name="bedtofilter" type="data" format="bed" optional="true" 40 <param name="bedtofilter" type="data" format="bed" optional="true"
77 label="Enable end-to-end alignments for mapping." 60 label="Enable end-to-end alignments for mapping."
78 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" /> 61 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
79 <param name="minMQ" type="integer" min="0" value="2" 62 <param name="minMQ" type="integer" min="0" value="2"
80 label="Minimum mapping quality" 63 label="Minimum mapping quality"
81 help="Minimum mapping quality to consider alignments (default: 2)." /> 64 help="Minimum mapping quality to consider alignments (default: 2)." />
82 <param name="minMQ" type="integer" label="Minimum mapping quality" min="0" value="2"
83 help="Minimum mapping quality to consider alignments (default: 2)." />
84 <param name="minID" type="float" min="0" value="0.95" 65 <param name="minID" type="float" min="0" value="0.95"
85 label="Minimum alignment identity" 66 label="Minimum alignment identity"
86 help="Minimum alignment-identity to consider alignments (default: 0.95)." /> 67 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
87 <param name="maxNM" type="integer" value="-1" 68 <param name="maxNM" type="integer" value="-1"
88 label="Maximum number of mismatches" 69 label="Maximum number of mismatches"
103 <param name="readLength" type="integer" min="50" value="50" 84 <param name="readLength" type="integer" min="50" value="50"
104 label="Read length" 85 label="Read length"
105 help="Maximum read length (before trimming)." /> 86 help="Maximum read length (before trimming)." />
106 </inputs> 87 </inputs>
107 <outputs> 88 <outputs>
108 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" /> 89 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/>
109 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" /> 90 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/>
91 <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/>
110 </outputs> 92 </outputs>
111 <tests> 93 <tests>
112 <test> 94 <test>
95 <!--Ensure default outputs work -->
113 <param name="reference_source_selector" value="history" /> 96 <param name="reference_source_selector" value="history" />
114 <param name="ref_file" value="ref.fa" /> 97 <param name="ref_file" value="ref.fa" />
115 <param name="Reference" value="actb.bed" /> 98 <param name="Reference" value="actb.bed" />
116 <param name="Reads" value="reads.fq" /> 99 <param name="Reads" value="reads.fq" />
117 <param name="readLength" value="100" /> 100 <param name="readLength" value="100" />
119 <param name="trim5" value="0" /> 102 <param name="trim5" value="0" />
120 </section> 103 </section>
121 <section name="advanced"> 104 <section name="advanced">
122 <param name="minBaseQual" value="27" /> 105 <param name="minBaseQual" value="27" />
123 </section> 106 </section>
124 <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv" 107 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
108 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
125 lines_diff="2" /> 109 lines_diff="2" />
110 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
126 </test> 111 </test>
127 <test> 112 <test>
128 <!-- test built-in fasta --> 113 <!--Ensure built-in fasta works -->
129 <param name="reference_source_selector" value="cached" /> 114 <param name="reference_source_selector" value="cached" />
130 <param name="Reference" value="actb.bed" /> 115 <param name="Reference" value="actb.bed" />
131 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> 116 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
132 <param name="readLength" value="100" /> 117 <param name="readLength" value="100" />
133 <section name="quantseq"> 118 <section name="quantseq">
134 <param name="trim5" value="0" /> 119 <param name="trim5" value="0" />
135 </section> 120 </section>
136 <section name="advanced"> 121 <section name="advanced">
137 <param name="minBaseQual" value="27" /> 122 <param name="minBaseQual" value="27" />
138 </section> 123 </section>
139 <output name="outputTsv" file="reads_slamdunk_mapped_filtered_tcount.tsv" 124 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
125 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
140 lines_diff="2" /> 126 lines_diff="2" />
127 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
141 </test> 128 </test>
142 </tests> 129 </tests>
143 <help><![CDATA[ 130 <help><![CDATA[
144 SLAM-seq 131 SLAM-seq
145 ======== 132 ========
160 **Reference** BED-file containing coordinates for 3' UTRs. 147 **Reference** BED-file containing coordinates for 3' UTRs.
161 **Reads** Sample FASTQ(gz) files. 148 **Reads** Sample FASTQ(gz) files.
162 **Read length** Maximum length of reads (usually 50, 100, 150). 149 **Read length** Maximum length of reads (usually 50, 100, 150).
163 =============== ========================================================================================================================================================== 150 =============== ==========================================================================================================================================================
164 151
165 This will run the entire *slamdunk* analysis with the most relevant output files being: 152 This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
166 153
167 * Tab-separated *tcount* file containing the SLAM-seq statistics per UTR 154 * Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
168 * BAM-file with the final mapped reads for visualization and further processing 155 * BAM-file with the final filtered mapped reads
156 * VCF file of variants called on the final filtered alignments
157
158 These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
169 159
170 ------------------------------------------------------ 160 ------------------------------------------------------
171 161
172 Multimapper recovery 162 Multimapper recovery
173 -------------------- 163 --------------------
196 Parameter Description 186 Parameter Description
197 ============================ ================================================================================ 187 ============================ ================================================================================
198 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read. 188 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
199 ============================ ================================================================================ 189 ============================ ================================================================================
200 190
191 .. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
201 192
202 ]]></help> 193 ]]></help>
203 <citations> 194 <citations>
204 <citation type="bibtex"> 195 <expand macro="citations" />
205 @misc{Neumann2018,
206 author = {Neumann, Tobias},
207 year = {2018},
208 title = Slamdunk},
209 publisher = {GitHub},
210 journal = {GitHub repository},
211 url = {https://github.com/t-neumann/slamdunk},
212 }
213 </citation>
214 </citations> 196 </citations>
215 </tool> 197 </tool>