Mercurial > repos > greg > vsnp_statistics
annotate vsnp_statistics.xml @ 6:429892a80419 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 16 Jun 2021 17:57:32 +0000 |
| parents | d0fbdeaaa488 |
| children | de2af65c4633 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@WRAPPER_VERSION@.1" profile="@PROFILE@"> |
| 0 | 2 <description></description> |
| 4 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 0 | 6 <requirements> |
|
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d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
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7 <requirement type="package" version="1.78">biopython</requirement> |
| 0 | 8 <requirement type="package" version="1.16.5">numpy</requirement> |
| 9 <requirement type="package" version="0.25.3">pandas</requirement> | |
| 1 | 10 <requirement type="package" version="1.2.0">xlrd</requirement> |
| 0 | 11 </requirements> |
| 12 <command detect_errors="exit_code"><![CDATA[ | |
| 13 #import re | |
| 14 #set input_idxstats_dir = 'input_idxstats' | |
| 15 #set input_metrics_dir = 'input_metrics' | |
| 16 #set input_reads_dir = 'input_reads' | |
| 17 mkdir -p $input_idxstats_dir && | |
| 18 mkdir -p $input_metrics_dir && | |
| 19 mkdir -p $input_reads_dir && | |
| 4 | 20 |
| 21 #if $input_type_cond.input_type == 'single_files': | |
| 22 #set read1 = $input_type_cond.read_type_cond.read1 | |
| 0 | 23 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) |
| 4 | 24 ln -s '${read1}' '${read1_identifier}' && |
| 25 #if $input_type_cond.read_type_cond.read_type == 'pair': | |
| 26 #set read2 = $input_type_cond.read_type_cond.read2 | |
| 27 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) | |
| 28 ln -s '${read2}' '${read2_identifier}' && | |
| 0 | 29 #else: |
| 4 | 30 #set read2 = None |
| 0 | 31 #end if |
| 32 #else: | |
| 4 | 33 #if $input_type_cond.collection_type_cond.collection_type == 'single': |
| 34 #for $i in $input_type_cond.collection_type_cond.reads_collection: | |
| 35 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) | |
| 36 ln -s '${i.file_name}' '$input_reads_dir/${identifier}' && | |
| 37 #end for | |
| 38 #else: | |
| 39 #set read1 = $input_type_cond.collection_type_cond.reads_collection['forward'] | |
| 40 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) | |
| 41 ln -s '${read1}' '$input_reads_dir/${read1_identifier}' && | |
| 42 #set read2 = $input_type_cond.collection_type_cond.reads_collection['reverse'] | |
| 43 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) | |
| 44 ln -s '${read2}' '$input_reads_dir/${read2_identifier}' && | |
| 45 #end if | |
| 46 #for $i in $input_type_cond.samtools_idxstats: | |
| 0 | 47 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) |
| 4 | 48 ln -s '${i.file_name}' '$input_idxstats_dir/${identifier}' && |
| 0 | 49 #end for |
| 4 | 50 #for $i in $input_type_cond.vsnp_azc: |
| 0 | 51 #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) |
| 4 | 52 ln -s '${i.file_name}' '$input_metrics_dir/${identifier}' && |
| 0 | 53 #end for |
| 54 #end if | |
| 4 | 55 |
| 0 | 56 python '$__tool_directory__/vsnp_statistics.py' |
| 4 | 57 #if $input_type_cond.input_type == 'single_files': |
| 58 --dbkey '$input_type_cond.samtools_idxstats.metadata.dbkey' | |
| 59 #if $input_type_cond.read_type_cond.read1.is_of_type('fastqsanger.gz'): | |
| 60 --gzipped | |
| 61 #end if | |
| 62 --read1 '${read1_identifier}' | |
| 63 #if $input_type_cond.read_type_cond.read_type == 'pair': | |
| 64 --read2 '${read2_identifier}' | |
| 0 | 65 #end if |
| 4 | 66 --samtools_idxstats '$input_type_cond.samtools_idxstats' |
| 67 --vsnp_azc '$input_type_cond.vsnp_azc' | |
| 68 #else: | |
| 69 --dbkey '$input_type_cond.samtools_idxstats[0].metadata.dbkey' | |
| 70 #if $input_type_cond.collection_type_cond.reads_collection[0].is_of_type('fastqsanger.gz'): | |
| 71 --gzipped | |
| 72 #end if | |
| 73 #if $input_type_cond.collection_type_cond.collection_type == 'paired': | |
| 74 --list_paired | |
| 75 #end if | |
| 76 --input_idxstats_dir '$input_idxstats_dir' | |
| 77 --input_metrics_dir '$input_metrics_dir' | |
| 78 --input_reads_dir '$input_reads_dir' | |
| 0 | 79 #end if |
| 1 | 80 --output '$output' |
| 0 | 81 ]]></command> |
| 82 <inputs> | |
| 83 <conditional name="input_type_cond"> | |
| 84 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> | |
| 4 | 85 <option value="single_files" selected="true">Single files</option> |
| 86 <option value="collections">Collections of files</option> | |
| 0 | 87 </param> |
| 4 | 88 <when value="single_files"> |
| 0 | 89 <conditional name="read_type_cond"> |
| 90 <param name="read_type" type="select" label="Choose the read type"> | |
| 4 | 91 <option value="single" selected="true">Single reads</option> |
| 92 <option value="pair">Paired reads</option> | |
| 0 | 93 </param> |
| 4 | 94 <when value="single"> |
| 95 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> | |
| 96 </when> | |
| 97 <when value="pair"> | |
| 0 | 98 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> |
| 99 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> | |
| 100 </when> | |
| 4 | 101 </conditional> |
| 102 <param name="samtools_idxstats" type="data" format="tabular" label="Samtools idxstats file"/> | |
| 103 <param name="vsnp_azc" type="data" format="tabular" label="vSNP: add zero coverage metrics file"/> | |
| 104 </when> | |
| 105 <when value="collections"> | |
| 106 <conditional name="collection_type_cond"> | |
| 107 <param name="collection_type" type="select" label="Collections of single reads or paired reads?"> | |
| 108 <option value="single" selected="true">Single reads</option> | |
| 109 <option value="paired">Paired reads in separate datasets</option> | |
| 110 </param> | |
| 0 | 111 <when value="single"> |
| 4 | 112 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="list" label="Collection of fastqsanger files"/> |
| 113 </when> | |
| 114 <when value="paired"> | |
| 115 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> | |
| 0 | 116 </when> |
| 117 </conditional> | |
| 4 | 118 <param name="samtools_idxstats" type="data_collection" format="tabular" collection_type="list" label="Collection of samtools idxstats files"/> |
| 119 <param name="vsnp_azc" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP: add zero coverage metrics files"/> | |
| 0 | 120 </when> |
| 121 </conditional> | |
| 122 </inputs> | |
| 123 <outputs> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
124 <data name="output" format="tabular"/> |
| 0 | 125 </outputs> |
| 126 <tests> | |
| 4 | 127 <!-- A single fastq file --> |
| 128 <test expect_num_outputs="1"> | |
| 129 <param name="input_type" value="single_files"/> | |
| 130 <param name="read_type" value="single"/> | |
| 131 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> | |
| 132 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/> | |
| 133 <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
134 <output name="output" file="vsnp_statistics1.tabular" ftype="tabular"/> |
| 4 | 135 </test> |
| 136 <!-- A set of paired fastq files --> | |
| 137 <test expect_num_outputs="1"> | |
| 138 <param name="input_type" value="single_files"/> | |
| 139 <param name="read_type" value="pair"/> | |
| 0 | 140 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> |
| 141 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> | |
| 4 | 142 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/> |
| 143 <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
144 <output name="output" file="vsnp_statistics2.tabular" ftype="tabular"/> |
| 4 | 145 </test> |
| 146 <!-- A collection of SE fastq files --> | |
| 147 <test expect_num_outputs="1"> | |
| 148 <param name="input_type" value="collections"/> | |
| 149 <param name="read_type" value="single"/> | |
| 150 <param name="reads_collection"> | |
| 151 <collection type="list"> | |
| 152 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="Mcap_Deer_DE_SRR650221.fastq.gz" dbkey="89"/> | |
| 153 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="13-1941-6_S4_L001_R1_600000.fastq.gz" dbkey="89"/> | |
| 154 </collection> | |
| 155 </param> | |
| 156 <param name="samtools_idxstats"> | |
| 157 <collection type="list"> | |
| 158 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="samtools_idxstats3.tabular" dbkey="89"/> | |
| 159 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="samtools_idxstats4.tabular" dbkey="89"/> | |
| 160 </collection> | |
| 161 </param> | |
| 162 <param name="vsnp_azc"> | |
| 163 <collection type="list"> | |
| 164 <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="add_zc_metrics3.tabular" dbkey="89"/> | |
| 165 <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/> | |
| 166 </collection> | |
| 167 </param> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
168 <output name="output" file="vsnp_statistics3.tabular" ftype="tabular"/> |
| 4 | 169 </test> |
| 170 <!-- A collection of PE fastq files --> | |
| 171 <test expect_num_outputs="1"> | |
| 172 <param name="input_type" value="collections"/> | |
| 173 <param name="collection_type" value="paired"/> | |
| 174 <param name="reads_collection"> | |
| 175 <collection type="paired"> | |
| 176 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> | |
| 177 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/> | |
| 178 </collection> | |
| 179 </param> | |
| 180 <param name="samtools_idxstats"> | |
| 181 <collection type="list"> | |
| 182 <element name="13-1941-6_S4_L001_R1_600000.fastq" value="samtools_idxstats5.tabular" dbkey="89"/> | |
| 183 </collection> | |
| 184 </param> | |
| 185 <param name="vsnp_azc"> | |
| 186 <collection type="list"> | |
| 187 <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/> | |
| 188 </collection> | |
| 189 </param> | |
|
5
d0fbdeaaa488
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"
greg
parents:
4
diff
changeset
|
190 <output name="output" file="vsnp_statistics4.tabular" ftype="tabular"/> |
| 0 | 191 </test> |
| 192 </tests> | |
| 193 <help> | |
| 194 **What it does** | |
| 195 | |
| 4 | 196 Accepts associated fastq files, SAMtools idxstats files and **vSNP: add zero coverage** metrics files and extracts information from them |
| 197 to produce an Excel spreadsheet containing statistics for each sample. The samples can be single or paired reads, and all associated inputs | |
| 198 can be either single files or collections of files. The output statistics include reference, file size, mean read length, mean read quality, | |
| 199 reads passing Q30, total reads, all mapped reads, unmapped reads, unmapped reads percentage of total, reference with coverage, average depth | |
| 200 of coverage and good SNP count. | |
| 0 | 201 </help> |
| 4 | 202 <expand macro="citations"/> |
| 0 | 203 </tool> |
| 204 |