| Next changeset 1:17ad142b56e6 (2021-10-05) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 3682ff4e2e47438e975fc04f92469eca7814fcfa" |
|
added:
bbmap.xml macros.xml test-data/13-1941-6_S4_L001_R1_600000.fastq.gz test-data/13-1941-6_S4_L001_R2_600000.fastq.gz test-data/NC_002945v4.fasta test-data/fasta_indexes.loc test-data/output1.bam test-data/output2.bam test-data/output3.bam tool-data/fasta_indexes.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 bbmap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bbmap.xml Mon Oct 04 12:14:47 2021 +0000 |
| [ |
| @@ -0,0 +1,157 @@ +<tool id="bbtools_bbmap" name="BBTools: BBMap" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>short-read aligner</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +#import os +#import re + +#if str($ref_source_cond.ref_source) == 'cached' + #set ref = str($ref_source_cond.reference.fields.path) +#else: + #set ref = $ref_source_cond.reference +#end if + +#if str($input_type_cond.input_type) in ['single', 'pair']: + #set read1 = $input_type_cond.read1 + #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) + ## bbmap uses the file extension to determine the input format. + #set ext = $read1_identifier + '.fastq' + #if $read1.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set read1_file = $read1_identifier + $ext + ln -s '${read1}' '${read1_file}' && + #if str($input_type_cond.input_type) == 'pair': + #set read2 = $input_type_cond.read2 + #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) + #set read2_file = $read2_identifier + $ext + ln -s '${read2}' '${read2_file}' && + #end if +#else: + #set read1 = $input_type_cond.reads_collection['forward'] + #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name)) + ## bbmap uses the file extension to determine the input format. + #set ext = $read1_identifier + '.fastq' + #if $read1.ext.endswith('.gz'): + #set ext = $ext + '.gz' + #end if + #set read1_file = $read1_identifier + $ext + ln -s '${read1}' '${read1_file}' && + #set read2 = $input_type_cond.reads_collection['reverse'] + #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name)) + #set read2_file = $read2_identifier + $ext + ln -s '${read2}' '${read2_file}' && +#end if + +bbmap.sh t=\${GALAXY_SLOTS:-4} ref='${ref}' +#if str($input_type_cond.input_type) == 'single': + in='${read1_file}' +#else: + in1='${read1_file}' in2='${read2_file}' +#end if +#if str($output_sort) == 'coordinate': + out='mapped.bam'; samtools sort -@\${GALAXY_SLOTS:-4} -T "\${TMPDIR:-.}" -O bam -o '$output' 'mapped.bam' +#elif str($output_sort) == 'name': + out='mapped.bam'; samtools sort -n -@\${GALAXY_SLOTS:-4} -T '\${TMPDIR:-.}' -O bam -o '$output' 'mapped.bam' +#else: + out='mapped.bam' && mv 'mapped.bam' '$output' +#end if +]]></command> + <inputs> + <conditional name="input_type_cond"> + <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> + <option value="single" selected="true">Single dataset</option> + <option value="pair">Dataset pair</option> + <option value="paired">List of dataset pairs</option> + </param> + <when value="single"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> + </when> + <when value="pair"> + <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> + <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> + </when> + <when value="paired"> + <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> + </when> + </conditional> + <expand macro="reference_source_cond"/> + <param name="output_sort" type="select" label="BAM sorting mode" help="The 'Not sorted' option can significantly extend the run time of the tool (it runs using a single thread)."> + <option value="coordinate" selected="True">Sort by chromosomal coordinates</option> + <option value="name">Sort by read names</option> + <option value="unsorted">Not sorted (sorted as input)</option> + </param> + </inputs> + <outputs> + <data format="bam" name="output" label="${tool.name} on ${on_string} (mapped reads in BAM format)"> + <expand macro="dbKeyActionsBBMap"/> + <change_format> + <when input="output_sort" value="name" format="qname_sorted.bam" /> + <when input="output_sort" value="unsorted" format="qname_input_sorted.bam" /> + </change_format> + </data> + </outputs> + <tests> + <!-- Single file, cached reference, output coordinate sorted --> + <test expect_num_outputs="1"> + <param name="input_type" value="single"/> + <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> + <output name="output" file="output1.bam" ftype="bam" lines_diff="4"> + <metadata name="dbkey" value="89" /> + </output> + </test> + <!-- Paired reads in separate datasets, cached reference, output name sorted --> + <test expect_num_outputs="1"> + <param name="input_type" value="pair"/> + <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> + <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> + <param name="output_sort" value="name"/> + <output name="output" file="output2.bam" ftype="qname_sorted.bam" lines_diff="4"> + <metadata name="dbkey" value="89" /> + </output> + </test> + <!-- Collection of Paired reads, history reference, output unsorted --> + <test expect_num_outputs="1"> + <param name="input_type" value="paired"/> + <param name="reads_collection"> + <collection type="paired"> + <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz"/> + <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz"/> + </collection> + </param> + <param name="ref_source" value="history"/> + <param name="reference" value="NC_002945v4.fasta" dbkey="89" ftype="fasta"/> + <param name="output_sort" value="unsorted"/> + <output name="output" file="output3.bam" ftype="qname_input_sorted.bam" lines_diff="4"> + <metadata name="dbkey" value="89" /> + </output> + </test> + </tests> + <help> +**What it does** + +BBMap is a splice-aware global aligner for DNA and RNA sequencing reads. It is fast and extremely accurate, particularly +with highly mutated genomes or reads with long indels, even whole-gene deletions over 100kbp long. It has no upper limit +to genome size or number of contigs and has been successfully used for mapping to an 85 gigabase soil metagenome with over +200 million contigs. the indexing phase is very fast compared to other aligners. + +BBMap can output many different statistics files; an empirical read quality histogram, insert-size distribution, and genome +coverage with or without generating a sam file. It is useful in quality control of libraries and sequencing runs or +evaluating new sequencing platforms. + +**Options** + + *Bam sorting mode* - the generated bam files can be sorted according to three criteria: coordinates, names and input order. + + * Sort by chromosomal coordinates - the file is sorted by coordinates (i.e., the reads from the beginning of the first + chromosome are first in the file. + * Sort by read names - the file is sorted by the reference ID (i.e., the QNAME field). + * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file. + + </help> + <expand macro="citations"/> +</tool> + |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 04 12:14:47 2021 +0000 |
| b |
| @@ -0,0 +1,63 @@ +<macros> + <token name="@WRAPPER_VERSION@">1.0.0</token> + <token name="@VERSION_SUFFIX@">1.0.0</token> + <token name="@PROFILE@">20.09</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="38.92">bbmap</requirement> + </requirements> + </xml> + <macro name="dbKeyActionsBBMap"> + <expand macro="dbKeyActions"> + <option type="from_data_table" name="fasta_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="ref_source_cond.reference" column="1"/> + </option> + </expand> + </macro> + <macro name="dbKeyActions"> + <actions> + <conditional name="ref_source_cond.ref_source"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <yield/> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/> + </action> + </when> + </conditional> + </actions> + </macro> + <macro name="reference_source_cond"> + <conditional name="ref_source_cond"> + <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history"> + <option value="cached" selected="True">Use a cached reference</option> + <option value="history">Use a reference from the history</option> + </param> + <when value="cached"> + <param name="reference" type="select" label="Using reference genome"> + <options from_data_table="fasta_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="A built-in reference genome is not available"/> + </options> + </param> + </when> + <when value="history"> + <param name="reference" type="data" format="fasta" label="Using reference genome"> + <validator type="no_options" message="The current history does not include a fasta dataset"/> + </param> + </when> + </conditional> + </macro> + <xml name="citations"> + <citations> + <citation type="doi"> + https://doi.org/10.1371/journal.pone.0185056 + </citation> + </citations> + </xml> +</macros> + |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/13-1941-6_S4_L001_R1_600000.fastq.gz |
| b |
| Binary file test-data/13-1941-6_S4_L001_R1_600000.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/13-1941-6_S4_L001_R2_600000.fastq.gz |
| b |
| Binary file test-data/13-1941-6_S4_L001_R2_600000.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/NC_002945v4.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_002945v4.fasta Mon Oct 04 12:14:47 2021 +0000 |
| b |
| @@ -0,0 +1,101 @@ +>NC_002945.4 Mycobacterium bovis AF2122/97 genome assembly, chromosome: Mycobacterium_bovis_AF2122/97 +TTGACCGATGACCCCGGTTCAGGCTTCACCACAGTGTGGAACGCGGTCGTCTCCGAACTTAACGGCGACC +CTAAGGTTGACGACGGACCCAGCAGTGATGCTAATCTCAGCGCTCCGCTGACCCCTCAGCAAAGGGCTTG +GCTCAATCTCGTCCAGCCATTGACCATCGTCGAGGGGTTTGCTCTGTTATCCGTGCCGAGCAGCTTTGTC +CAAAACGAAATCGAGCGCCATCTGCGGGCCCCGATTACCGACGCTCTCAGCCGCCGACTCGGACATCAGA +TCCAACTCGGGGTCCGCATCGCTCCGCCGGCGACCGACGAAGCCGACGACACTACCGTGCCGCCTTCCGA +AAATCCTGCTACCACATCGCCAGACACCACAACCGACAACGACGAGATTGATGACAGCGCTGCGGCACGG +GGCGATAACCAGCACAGTTGGCCAAGTTACTTCACCGAGCGCCCGCGCAATACCGATTCCGCTACCGCTG +GCGTAACCAGCCTTAACCGTCGCTACACCTTTGATACGTTCGTTATCGGCGCCTCCAACCGGTTCGCGCA +CGCCGCCGCCTTGGCGATCGCAGAAGCACCCGCCCGCGCTTACAACCCCCTGTTCATCTGGGGCGAGTCC +GGTCTCGGCAAGACACACCTGCTACACGCGGCAGGCAACTATGCCCAACGGTTGTTCCCGGGAATGCGGG +TCAAATATGTCTCCACCGAGGAATTCACCAACGACTTCATTAACTCGCTCCGCGATGACCGCAAGGTCGC +ATTCAAACGCAGCTACCGCGACGTAGACGTGCTGTTGGTCGACGACATCCAATTCATTGAAGGCAAAGAG +GGTATTCAAGAGGAGTTCTTCCACACCTTCAACACCTTGCACAATGCCAACAAGCAAATCGTCATCTCAT +CTGACCGCCCACCCAAGCAGCTCGCCACCCTCGAGGACCGGCTGAGAACCCGCTTTGAGTGGGGGCTGAT +CACTGACGTACAACCACCCGAGCTGGAGACCCGCATCGCCATCTTGCGCAAGAAAGCACAGATGGAACGG +CTCGCGATCCCCGACGATGTCCTCGAACTCATCGCCAGCAGTATCGAACGCAATATCCGTGAACTCGAGG +GCGCGCTGATCCGGGTCACCGCGTTCGCCTCATTGAACAAAACACCAATCGACAAAGCGCTGGCCGAGAT +TGTGCTTCGCGATCTGATCGCCGACGCCAACACCATGCAAATCAGCGCGGCGACGATCATGGCTGCCACC +GCCGAATACTTCGACACTACCGTCGAAGAGCTTCGCGGGCCCGGCAAGACCCGAGCACTGGCCCAGTCAC +GACAGATTGCGATGTACCTGTGTCGTGAGCTCACCGATCTTTCGTTGCCCAAAATCGGCCAAGCGTTCGG +CCGTGATCACACAACCGTCATGTACGCCCAACGCAAGATCCTGTCCGAGATGGCCGAGCGCCGTGAGGTC +TTTGATCACGTCAAAGAACTCACCACTCGCATCCGTCAGCGCTCCAAGCGCTAGCACGGCGTGTTCTTCC +GACAACGTTCTTAAAAAAACTTCTCTCTCCCAGGTCACACCAGTCACAGAGATTGGCTGTGAGTGTCGCT +GTGCACAAACCGCGCACAGACTCATACAGTCCCGGCGGTTCCGTTCACAACCCACGCCTCATCCCCACCG +ACCCAACACACACCCCACAGTCATCGCCACCGTCATCCACAACTCCGACCGACGTCGACCTGCACCAAGA +CCAGACTGTCCCCAAACTGCACACCCTCTAATACTGTTACCGAGATTTCTTCGTCGTTTGTTCTTGGAAA +GACAGCGCTGGGGATCGTTCGCTGGATACCACCCGCATAACTGGCTCGTCGCGGTGGGTCAGAGGTCAAT +GATGAACTTTCAAGTTGACGTGAGAAGCTCTACGGTTGTTGTTCGACTGCTGTTGCGGCCGTCGTGGCGG +GTCACGCGTCATGGGCGTTCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTAGCCACGGGATCGAACTC +ATCGTGAGGTGAAAGGGCGCAATGGACGCGGCTACGACAAGAGTTGGCCTCACCGACTTGACGTTTCGTT +TGCTACGAGAGTCTTTCGCCGATGCGGTGTCGTGGGTGGCTAAAAATCTGCCAGCCAGGCCCGCGGTGCC +GGTGCTCTCCGGCGTGTTGTTGACCGGCTCGGACAACGGTCTGACGATTTCCGGATTCGACTACGAGGTT +TCCGCCGAGGCCCAGGTTGGCGCTGAAATTGTTTCTCCTGGAAGCGTTTTAGTTTCTGGCCGATTGTTGT +CCGATATTACCCGGGCGTTGCCTAACAAGCCCGTAGGCGTTCATGTCGAAGGTAACCGGGTCGCATTGAC +CTGCGGTAACGCCAGGTTTTCGCTACCGACGATGCCAGTCGAGGATTATCCGACGCTGCCGACGCTGCCG +GAAGAGACCGGATTGTTGCCTGCGGAATTATTCGCCGAGGCAATCAGTCAGGTCGCTATCGCCGCCGGCC +GGGACGACACGCTGCCTATGTTGACCGGCATCCGGGTCGAAATCCTCGGTGAGACGGTGGTTTTGGCCGC +TACCGACAGGTTTCGCCTGGCTGTTCGAGAACTGAAGTGGTCGGCGTCGTCGCCAGATATCGAAGCGGCT +GTGCTGGTCCCGGCCAAGACGCTGGCCGAGGCCGCCAAAGCGGGCATCGGCGGCTCTGACGTTCGTTTGT +CGTTGGGTACTGGGCCGGGGGTGGGCAAGGATGGCCTGCTCGGTATCAGTGGGAACGGCAAGCGCAGCAC +CACGCGACTTCTTGATGCCGAGTTCCCGAAGTTTCGGCAGTTGCTACCAACCGAACACACCGCGGTGGCC +ACCATGGACGTGGCCGAGTTGATCGAAGCGATCAAGCTGGTTGCGTTGGTAGCTGATCGGGGCGCGCAGG +TGCGCATGGAGTTCGCTGATGGCAGCGTGCGGCTTTCTGCGGGTGCCGATGATGTTGGACGAGCCGAGGA +AGATCTTGTTGTTGACTATGCCGGTGAACCATTGACGATTGCGTTTAACCCAACCTATCTAACGGACGGT +TTGAGTTCGTTGCGCTCGGAGCGAGTGTCTTTCGGGTTTACGACTGCGGGTAAGCCTGCCTTGCTACGTC +CGGTGTCCGGGGACGATCGCCCTGTGGCGGGTCTGAATGGCAACGGTCCGTTCCCGGCGGTGTCGACGGA +CTATGTCTATCTGTTGATGCCGGTTCGGTTGCCGGGCTGAGCACTTGGCGCCCGGGTAGGTGTACGTCCG +TCATTTGGGGCTGCGTGACTTCCGGTCCTGGGCATGTGTAGATCTGGAATTGCATCCAGGGCGGACGGTT +TTTGTTGGGCCTAACGGTTATGGTAAGACGAATCTTATTGAGGCACTGTGGTATTCGACGACGTTAGGTT +CGCACCGCGTTAGCGCCGATTTGCCGTTGATCCGGGTAGGTACCGATCGTGCGGTGATCTCCACGATCGT +GGTGAACGACGGTAGAGAATGTGCCGTCGACCTCGAGATCGCCACGGGGCGAGTCAACAAAGCGCGATTG +AATCGATCATCGGTCCGAAGTACACGTGATGTGGTCGGAGTGCTTCGAGCTGTGTTGTTTGCCCCTGAGG +ATCTGGGGTTGGTTCGTGGGGATCCCGCTGACCGGCGGCGCTATCTGGATGATCTGGCGATCGTGCGTAG +GCCTGCGATCGCTGCGGTACGAGCCGAATATGAGAGGGTGGTGCGCCAGCGGACGGCGTTATTGAAGTCC +GTACCTGGAGCACGGTATCGGGGTGACCGGGGTGTGTTTGACACTCTTGAGGTATGGGACAGTCGTTTGG +CGGAGCACGGGGCTGAACTGGTGGCCGCCCGCATCGATTTGGTCAACCAGTTGGCACCGGAAGTGAAGAA +GGCATACCAGCTGTTGGCGCCGGAATCGCGATCGGCGTCTATCGGTTATCGGGCCAGCATGGATGTAACC +GGTCCCAGCGAGCAGTCAGATACCGATCGGCAATTGTTAGCAGCTCGGCTGTTGGCGGCGCTGGCGGCCC +GTCGGGATGCCGAACTCGAGCGTGGGGTTTGTCTAGTTGGTCCGCACCGTGACGACCTAATACTGCGACT +AGGCGATCAACCCGCGAAAGGATTTGCTAGCCATGGGGAGGCGTGGTCGTTGGCGGTGGCACTGCGGTTG +GCGGCCTATCAACTGTTACGCGTTGATGGTGGTGAGCCGGTGTTGTTGCTCGACGACGTGTTCGCCGAAC +TGGATGTCATGCGCCGTCGAGCGTTGGCGACGGCGGCCGAGTCCGCCGAACAGGTGTTGGTGACTGCCGC +GGTGCTCGAGGATATTCCCGCCGGCTGGGACGCCAGGCGGGTGCACATCGATGTGCGTGCCGATGACACC +GGATCGATGTCGGTGGTTCTGCCATGACGGGTTCTGTTGACCGGCCCGACCAGAATCGCGGTGAGCGATT +AATGAAGTCACCAGGGTTGGATTTGGTCAGGCGCACCCTGGACGAAGCTCGTGCTGCTGCCCGCGCGCGC +GGACAAGACGCCGGTCGAGGGCGGGTCGCTTCCGTTGCGTCGGGTCGGGTGGCCGGACGGCGACGAAGCT +GGTCGGGTCCGGGGCCCGACATTCGTGATCCACAACCGCTGGGTAAGGCCGCTCGTGAGCTGGCAAAGAA +ACGCGGCTGGTCGGTGCGGGTCGCCGAGGGTATGGTGCTCGGCCAGTGGTCTGCGGTGGTCGGCCACCAG +ATCGCCGAACATGCACGCCCGACTGCGCTAAACGACGGGGTGTTGAGCGTGATTGCGGAGTCGACGGCGT +GGGCGACGCAGTTGAGGATCATGCAGGCCCAGCTTCTGGCCAAGATCGCCGCAGCGGTTGGCAACGATGT +GGTGCGATCGCTAAAGATCACCGGGCCGGCGGCACCATCGTGGCGCAAGGGGCCTCGCCATATTGCCGGT +AGGGGTCCGCGCGACACCTACGGATAACACGTCGATCGGCCCAGAACAAGGCGCTCCGGTCCCGGCCTGA +GAGCCTCGAGGACGAAGCGGATCCGTATGCCGGACGTCGGGACGCACCAGGAAGAAAGATGTCCGACGCA +CGGCGCGGTTAGATGGGTAAAAACGAGGCCAGAAGATCGGCCCTGGCGCCCGATCACGGTACAGTGGTGT +GCGACCCCCTGCGGCGACTCAACCGCATGCACGCAACCCCTGAGGAGAGTATTCGGATCGTGGCTGCCCA +GAAAAAGAAGGCCCAAGACGAATACGGCGCTGCGTCTATCACCATTCTCGAAGGGCTGGAGGCCGTCCGC +AAACGTCCCGGCATGTACATTGGCTCGACCGGTGAGCGCGGTTTACACCATCTCATTTGGGAGGTGGTCG +ACAACGCGGTCGACGAGGCGATGGCCGGTTATGCAACCACAGTGAACGTAGTGCTGCTTGAGGATGGCGG +TGTCGAGGTCGCCGACGACGGCCGCGGCATTCCGGTCGCCACCCACGCCTCCGGCATACCGACCGTCGAC +GTGGTGATGACACAACTACATGCCGGCGGCAAGTTCGACTCGGACGCGTATGCGATATCTGGTGGTCTGC +ACGGCGTCGGCGTGTCGGTGGTTAACGCGCTATCCACCCGGCTCGAAGTCGAGATCAAGCGCGACGGGTA +CGAGTGGTCTCAGGTTTATGAGAAGTCGGAACCCCTGGGCCTCAAGCAAGGGGCGCCGACCAAGAAGACG +GGGTCAACGGTACGGTTCTGGGCCGACCCCGCTGTTTTCGAAACCACGGAATACGACTTCGAAACCGTCG +CCCGCCGGCTGCAAGAGATGGCGTTCCTCAACAAGGGGCTGACCATCAACCTGACCGACGAGAGGGTGAC +CCAAGACGAGGTCGTCGACGAAGTGGTCAGCGACGTCGCCGAGGCGCCGAAGTCGGCAAGTGAACGCGCA +GCCGAATCCACTGCACCGCACAAAGTTAAGAGCCGCACCTTTCACTATCCGGGTGGCCTGGTGGACTTCG +TGAAACACATCAACCGCACCAAGAACGCGATTCATAGCAGCATCGTGGACTTTTCCGGCAAGGGCACCGG +GCACGAGGTGGAGATCGCGATGCAATGGAACGCCGGGTATTCGGAGTCGGTGCACACCTTCGCCAACACC +ATCAACACCCACGAGGGCGGCACCCACGAAGAGGGCTTCCGCAGCGCGCTGACGTCGGTGGTGAACAAGT +ACGCCAAGGACCGCAAGCTACTGAAGGACAAGGACCCCAACCTCACCGGTGACGATATCCGGGAAGGCCT +GGCCGCTGTGATCTCGGTGAAGGTCAGCGAACCGCAGTTCGAGGGCCAGACCAAGACCAAGTTGGGCAAC +ACCGAGGTCAAATCGTTTGTGCAGAAGGTCTGTAATGAACAGCTGACCCACTGGTTTGAAGCCAACCCCA +CCGACTCGAAAGTCGTTGTGAACAAGGCTGTGTCCTCGGCGCAAGCCCGTATCGCGGCACGTAAGGCACG +AGAGTTGGTGCGGCGTAAGAGCGCCACCGACATCGGTGGATTGCCCGGCAAGCTGGCCGATTGCCGTTCC +ACGGATCCGCGCAAGTCCGAACTGTATGTCGTAGAAGGTGACTCGGCCGGCGGTTCTGCAAAAAGCGGTC +GCGATTCGATGTTCCAGGCGATACTTCCGCTGCGCGGCAAGATCATCAATGTGGAGAAAGCGCGCATCGA +CCGGGTGCTAAAGAACACCGAAGTTCAGGCGATCATCACGGCGCTGGGCACCGGGATCCACGACGAGTTC +GATATCGGCAAGCTGCGCTACCACAAGATCGTGCTGATGGCCGACGCCGATGTTGACGGCCAACATATTT +CCACGCTGTTGTTGACGTTGTTGTTCCGGTTCATGCGGCCGCTCATCGAGAACGGGCATGTGTTTTTGGC +ACAACCGCCGCTGTACAAACTCAAGTGGCAGCGCAGTGACCCGGAATTCGCATACTCCGACCGCGAGCGC |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/fasta_indexes.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fasta_indexes.loc Mon Oct 04 12:14:47 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +89 89 Mycobacterium_AF2122 ${__HERE__}/NC_002945v4.fasta |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/output1.bam |
| b |
| Binary file test-data/output1.bam has changed |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/output2.bam |
| b |
| Binary file test-data/output2.bam has changed |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 test-data/output3.bam |
| b |
| Binary file test-data/output3.bam has changed |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 tool-data/fasta_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/fasta_indexes.loc.sample Mon Oct 04 12:14:47 2021 +0000 |
| b |
| @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a fasta_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The fasta_indexes.loc +#file has this format (white space characters are TAB characters): +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg19 Canonical indexed stored in +# +# /depot/data2/galaxy/hg19/sam/, +# +#then the fasta_indexes.loc entry would look like this: +# +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +# +#and your /depot/data2/galaxy/hg19/sam/ directory +#would contain hg19canon.fa and hg19canon.fa.fai files. +# +#Your fasta_indexes.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa +#hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Oct 04 12:14:47 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Location of SAMTools indexes for FASTA files --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 07a6e49c7d74 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Oct 04 12:14:47 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> |