Mercurial > repos > iuc > slamdunk
comparison slamdunk.xml @ 2:fae4a5ec0653 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 0c32e3f0d4de0c3f560b02aff98ed8550f69d6c3
author | iuc |
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date | Mon, 21 Jan 2019 07:34:47 -0500 |
parents | 57bf9a0d49a5 |
children | 24657d5edede |
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1:57bf9a0d49a5 | 2:fae4a5ec0653 |
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1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1"> | 1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy2"> |
2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description> | 2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
7 <version_command>slamdunk --version</version_command> | 7 <version_command>slamdunk --version</version_command> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 #if $reference_source.reference_source_selector == 'history': | 9 #import re |
10 ln -f -s '$reference_source.ref_file' reference.fa && | 10 |
11 #else: | 11 #if $reference_source.reference_source_selector == 'history': |
12 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && | 12 ln -f -s '$reference_source.ref_file' reference.fa && |
13 #end if | 13 #else: |
14 slamdunk all -r reference.fa -b '$Reference' -o ./out | 14 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && |
15 -n $multimapper.multimappers | 15 #end if |
16 $multimapper.multimap | 16 |
17 #if $multimapper.filterbed.bedtofilter: | 17 mkdir ./fastq && |
18 -fb $multimapper.filterbed.bedtofilter | 18 #for $fastq in $reads: |
19 #end if | 19 #set $fastq_name = re.sub('[^\w\-\.]', '_', str($fastq.element_identifier)) |
20 -5 $quantseq.trim5 | 20 ln -s '$fastq' './fastq/${fastq_name}' && |
21 -a $quantseq.maxpolyA | 21 #end for |
22 $advanced.endtoend | 22 |
23 -mq $advanced.minMQ | 23 slamdunk all -r reference.fa -b '$Reference' -o ./out |
24 -mi $advanced.minID | 24 -n $multimapper.multimappers |
25 -nm=$advanced.maxNM | 25 $multimapper.multimap |
26 -mc $advanced.minCov | 26 #if $multimapper.filterbed.bedtofilter: |
27 -mv $advanced.minVar | 27 -fb $multimapper.filterbed.bedtofilter |
28 -mbq $advanced.minBaseQual | 28 #end if |
29 -rl $readLength | 29 -5 $quantseq.trim5 |
30 -c $covThresh | 30 -a $quantseq.maxpolyA |
31 '$Reads' | 31 $advanced.endtoend |
32 -mq $advanced.minMQ | |
33 -mi $advanced.minID | |
34 -nm=$advanced.maxNM | |
35 -mc $advanced.minCov | |
36 -mv $advanced.minVar | |
37 -mbq $advanced.minBaseQual | |
38 -rl $readLength | |
39 -c $covThresh | |
40 ./fastq/* | |
32 ]]></command> | 41 ]]></command> |
33 <inputs> | 42 <inputs> |
34 <expand macro="reference_files" /> | 43 <expand macro="reference_files" /> |
35 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/> | 44 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" multiple="True" label="FASTQ files"/> |
36 <section name="multimapper" title="Multimapper recovery" | 45 <section name="multimapper" title="Multimapper recovery" |
37 expanded="false"> | 46 expanded="false"> |
38 <section name="filterbed" | 47 <section name="filterbed" |
39 title="Use separate 3' UTR bed to filter multimappers." expanded="false"> | 48 title="Use separate 3' UTR bed to filter multimappers." expanded="false"> |
40 <param name="bedtofilter" type="data" format="bed" optional="true" | 49 <param name="bedtofilter" type="data" format="bed" optional="true" |
84 <param name="readLength" type="integer" min="50" value="50" | 93 <param name="readLength" type="integer" min="50" value="50" |
85 label="Read length" | 94 label="Read length" |
86 help="Maximum read length (before trimming)." /> | 95 help="Maximum read length (before trimming)." /> |
87 </inputs> | 96 </inputs> |
88 <outputs> | 97 <outputs> |
89 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/> | 98 <collection name="outputBam" type="list" label="${tool.name} on ${on_string}: BAM"> |
90 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/> | 99 <discover_datasets pattern="(?P<name>.+)\.bam$" format="bam" directory="./out/filter" visible="false" /> |
91 <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/> | 100 </collection> |
101 <collection name="outputTsv" type="list" label="${tool.name} on ${on_string}: Count TSV"> | |
102 <discover_datasets pattern="(?P<name>.+)_tcount.tsv$" format="tabular" directory="./out/count" visible="false" /> | |
103 </collection> | |
104 <collection name="outputVcf" type="list" label="${tool.name} on ${on_string}: VCF"> | |
105 <discover_datasets pattern="(?P<name>.+)_snp.vcf$" format="vcf" directory="./out/snp" visible="false" /> | |
106 </collection> | |
92 </outputs> | 107 </outputs> |
93 <tests> | 108 <tests> |
94 <test> | 109 <test> |
95 <!--Ensure default outputs work --> | 110 <!--Ensure default outputs work --> |
96 <param name="reference_source_selector" value="history" /> | 111 <param name="reference_source_selector" value="history" /> |
97 <param name="ref_file" value="ref.fa" /> | 112 <param name="ref_file" value="ref.fa" /> |
98 <param name="Reference" value="actb.bed" /> | 113 <param name="Reference" value="actb.bed" /> |
99 <param name="Reads" value="reads.fq" /> | 114 <param name="reads" value="reads.fq" /> |
100 <param name="readLength" value="100" /> | 115 <param name="readLength" value="100" /> |
101 <section name="quantseq"> | 116 <section name="quantseq"> |
102 <param name="trim5" value="0" /> | 117 <param name="trim5" value="0" /> |
103 </section> | 118 </section> |
104 <section name="advanced"> | 119 <section name="advanced"> |
105 <param name="minBaseQual" value="27" /> | 120 <param name="minBaseQual" value="27" /> |
106 </section> | 121 </section> |
107 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> | 122 <output_collection name="outputBam"> |
108 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" | 123 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> |
109 lines_diff="2" /> | 124 </output_collection> |
110 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> | 125 <output_collection name="outputTsv"> |
126 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" | |
127 lines_diff="2" /> | |
128 </output_collection> | |
129 <output_collection name="outputVcf"> | |
130 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> | |
131 </output_collection> | |
111 </test> | 132 </test> |
112 <test> | 133 <test> |
113 <!--Ensure built-in fasta works --> | 134 <!--Ensure built-in fasta works --> |
114 <param name="reference_source_selector" value="cached" /> | 135 <param name="reference_source_selector" value="cached" /> |
115 <param name="Reference" value="actb.bed" /> | 136 <param name="Reference" value="actb.bed" /> |
116 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> | 137 <param name="reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" /> |
117 <param name="readLength" value="100" /> | 138 <param name="readLength" value="100" /> |
118 <section name="quantseq"> | 139 <section name="quantseq"> |
119 <param name="trim5" value="0" /> | 140 <param name="trim5" value="0" /> |
120 </section> | 141 </section> |
121 <section name="advanced"> | 142 <section name="advanced"> |
122 <param name="minBaseQual" value="27" /> | 143 <param name="minBaseQual" value="27" /> |
123 </section> | 144 </section> |
124 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/> | 145 <output_collection name="outputBam"> |
125 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" | 146 <element name="reads_slamdunk_mapped_filtered" ftype="bam" file="reads1.bam" compare="sim_size" /> |
126 lines_diff="2" /> | 147 </output_collection> |
127 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/> | 148 <output_collection name="outputTsv"> |
149 <element name="reads_slamdunk_mapped_filtered" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv" | |
150 lines_diff="2" /> | |
151 </output_collection> | |
152 <output_collection name="outputVcf"> | |
153 <element name="reads_slamdunk_mapped_filtered" ftype="vcf" file="reads1_snp.vcf" compare="sim_size" /> | |
154 </output_collection> | |
128 </test> | 155 </test> |
129 </tests> | 156 </tests> |
130 <help><![CDATA[ | 157 <help><![CDATA[ |
131 SLAM-seq | 158 SLAM-seq |
132 ======== | 159 ======== |