| Next changeset 1:12fc62b7dc09 (2015-02-12) |
|
Commit message:
Imported from capsule None |
|
added:
mapper.xml test-data/cel_cluster.fa test-data/reads.fa tool-data/bowtie_indices.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| b |
| diff -r 000000000000 -r af18bb0baa92 mapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mapper.xml Tue Jan 27 09:06:06 2015 -0500 |
| [ |
| b'@@ -0,0 +1,208 @@\n+<tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0">\n+ <macros>\n+ <macro name="map_params">\n+ <conditional name="refGenomeSource">\n+ <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin.">\n+ <options from_data_table="bowtie_indexes">\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n+ </options>\n+ </param>\n+ </when> <!-- build-in -->\n+ <when value="history">\n+ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />\n+ </when> <!-- history -->\n+ </conditional> <!-- refGenomeSource -->\n+ <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/>\n+ <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)">\n+ <validator type="in_range" min="1" message="Minimum value is 1"/>\n+ </param>\n+ </macro>\n+ </macros>\n+ <description>\n+<![CDATA[\n+process and map reads to a reference genome\n+]]>\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="2.0">mirdeep2_mapper</requirement>\n+ <requirement type="package" version="0.12.7">bowtie</requirement>\n+ <requirement type="package" version="5.18.1">perl</requirement>\n+ </requirements>\n+\n+ <command>\n+<![CDATA[\n+\n+ #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"\n+ #if $operation.refGenomeSource.genomeSource == "history"\n+ bowtie-build $operation.refGenomeSource.ownFile custom_bowtie_indices &&\n+ #end if\n+ #end if\n+ mapper.pl \n+ \n+ $reads\n+ \n+ #if $reads.extension.startswith("fasta")\n+ -c\n+ #else if $reads.extension.startswith("fastq")\n+ -e -h\n+ #end if\n+\n+ $remove_non_canon\n+ \n+ $convert_rna_dna\n+\n+ #if $clip_adapter.clip == "true"\n+ -k $clip_adapter.adapter_seq\n+ #end if\n+\n+ -l $discard_short_reads\n+\n+ #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse"\n+ -m -s $output_reads_collapsed\n+ #end if\n+ \n+ #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"\n+ -p \n+ \n+ #if $operation.refGenomeSource.genomeSource == "history"\n+ custom_bowtie_indices\n+ #else\n+ $index\n+ #end if\n+\n+ $operation.map_mismatch\n+\n+ -r $operation.map_threshold\n+ \n+ -t $output_mapping\n+ #end if\n+\n+ -v -n\n+]]>\n+ </command>\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ <inputs>\n+ <param forma'..b' <expand macro="map_params"/>\n+ </when>\n+ <when value="only_collapse"/>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="fasta" name="output_reads_collapsed" label="Collapsed reads of ${tool.name} on ${on_string}">\n+ <filter>\n+ (\n+ operation[\'collapse_map\'] == "collapse_and_map" or\n+ operation[\'collapse_map\'] == "only_collapse"\n+ )\n+ </filter>\n+ </data>\n+ <data format="tabular" name="output_mapping" label="Mapping output of ${tool.name} on ${on_string} in ARF format">\n+ <filter>\n+ (\n+ operation[\'collapse_map\'] == "collapse_and_map" or\n+ operation[\'collapse_map\'] == "only_map"\n+ )\n+ </filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="reads" value="reads.fa"/>\n+ <param name="remove_non_canon" value="True"/>\n+ <param name="clip" value="true"/>\n+ <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/>\n+ <param name="discard_short_reads" value="18"/>\n+ <param name="collapse_map" value="collapse_and_map"/>\n+ <param name="genomeSource" value="history"/>\n+ <param name="ownFile" value="cel_cluster.fa"/>\n+ <output name="output_reads_collapsed">\n+ <assert_contents>\n+ <has_text text=">seq_349713_x268"/>\n+ <has_text text="TCACCGGGTGTANATCAGCTAA"/>\n+ <has_text text=">seq_354255_x214"/>\n+ <has_text text="TAACCGGGTGAACACTTGCAGT"/>\n+ <has_text text=">seq_357284_x187"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_mapping">\n+ <assert_contents>\n+ <has_line_matching expression="^.*22\\t1\\t22\\ttcaccgggtggaaactagcagt\\tchrII:11534525-11540624\\t22\\t3060\\t3081.*$"/>\n+ <has_line_matching expression="^.*22\\t1\\t22\\ttcaccgggtggaaactagtagt\\tchrII:11534525-11540624\\t22\\t3060\\t3081.*$"/>\n+ <has_line_matching expression="^.*22\\t1\\t22\\ttcaccgggtgtacatcagcgaa\\tchrII:11534525-11540624\\t22\\t3631\\t3652.*$"/>\n+ <has_line_matching expression="^.*22\\t1\\t22\\ttcaccgggagaaaaactggtgt\\tchrII:11534525-11540624\\t22\\t3382\\t3403.*$"/>\n+ <has_line_matching expression="^.*25\\t1\\t25\\ttcaccgggtggaaactagcagtggc\\tchrII:11534525-11540624\\t25\\t3060\\t3084.*$"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+**What MiRDeep2 Mapper does**\n+\n+The mapper module is designed as a tool to process deep sequencing reads and/or map them to the reference genome. \n+The module works in sequence space, and can process or map data that is in sequence fasta format. \n+A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind.\n+\n+**Example**\n+\n+Processing reads and mapping them to a genome.\n+\n+The -c option designates that the input file is a fasta file. The -j options removes entries with\n+non-canonical letters (letters other than a,c,g,t,u,n,A,C,G,T,U,N). The -k option clips adapters. The -l option discards reads shorter than 18 nts.\n+The -m option collapses the reads. The -p option maps the processed reads against the previously indexed genome (cel_cluster). The -s option\n+designates the name of the output file of processed reads and the -t option designates the name of the output file of the genome mappings. Last,\n+-v gives verbose output to the screen.\n+\n+ ``mapper.pl reads.fa -c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -p cel_cluster -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v``\n+\n+]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkr688</citation>\n+ <citation type="doi">10.1002/0471250953.bi1210s36</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r af18bb0baa92 test-data/cel_cluster.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cel_cluster.fa Tue Jan 27 09:06:06 2015 -0500 |
| b |
| @@ -0,0 +1,132 @@ +>chrII:11534525-11540624 +tccaaaatattagaggccccacgaaaaggggagcagaacgaaaaggggat +ctgcaaaaaggggatctgcgaaaaggggagatacgaaaaggggagatacg +aaaaggggagcaacgaaaaggggatctggcactgtgccaaacgctatttt +tctcaaagaaaacaatacaacgatgctccgatgttacgcgtcgcgtgttg +ttaagcgtatcttctagaagaaaatttcaaaaatcaacgtgcgttgcgtg +agaaaaattgcgttttgtgcgtttggcacagtgccagctccccttttcgt +tgctccccttttcgtatctccccttttcgtatctccccttttcgcagatc +ccctttttgcagatccccttttcgttctgctcccctcgtggggcctcaaa +taatattgtcaatggagcgcagttgcgcacaccgaaatacgcacgaaatt +tgaaattggcaggcctagaaagtctggatttaaaatatttatgcatatta +acctgagtttcggcatgtttagataaatttagattaaaatttattaaata +aaaatatttaaaatttattaaattcaacattatctttaattttacagaaa +taaaaaccaaaaaaccaacgaagtgtaacttttcgacaataaatatttat +aaattattcaattaattggaaatctatttatcacatctcatcgtgaacaa +gcacatggctaaacaatgcctcgactttatccacccatcctggatttttc +ctgttgaaaatcttcaaatccttcatagtctgctcaattgccttaacagc +cttttcccttttcacatccttcgtcaattcctcaaccatcgcctctacaa +gttgtgatcgtgaggccccttcaacgaatttcttgtccaatacatctctg +agctgaaaaataagtccctttattcatgtgcaccacctgccactcattca +ttttagatcctaatcctgtatttctctctctctctcactaatcgtcccgt +catatctgacccactataatgaggggaccaccactttgccccagatttcg +taatgagccaacatacactaggccctgttctagcacccccattgtgcatg +ggagacacatcgtctgttggttcgggtcagctgagatgacgtggcagatg +acgtcatgtttgttctctagcagatccctatcgtaaaataccgttctttg +ttcgtttatgagcacttcttgggaaacaagaagaatattagagaatattg +gattttaggaaatttcttgaccctaataatatgtatctcatggggctaat +tacgaaagatttagagctcactaaagcagatgtggataagctggaactat +agtcaattctcacgagatattattattagcttactcgttgaatttgatgc +cgtgttaggtagaagccgagaacacgatgaaccttggaagttatgtagtc +gagttttctggaagaaaaagtatatatagtttgataaaaagttacgtcat +aagttattggtcccgagtgtgtacactagaaacttgcgcaatcagttggt +caggtggtctaggacctttacatgtaatataattcattggtttgttgctc +tagatctcaaagaatatggttttcctgctgagaaacaaaatttttttttc +aaatgttcgcgatattatacgatttttttgcgctgaaaaatacggtatcc +ggactcgacacgacagtttttcaataaattcggaaaggtacatatgcgcc +tttgaagagtactgtaattttaaacatttgttgatgcagtaaatattctc +acggatttttagaggtttttttttgaatatttatacagttatattagagt +taaaaaaataaatctatttttatcgaaatttatgaaaaatctactcccca +gaaacaaagtttgaatttacttaaaatgtatgtgcgcctttttaaattca +acaaaaatttatcaaattttgtctttttaatcacttttacttttttttcg +aaaaaaaaaaaaactttaaaaacaccgaaaattaaaatttttaattaccg +taatcctttaaaggcgcacacctctttttcgcaatcataaaaatttacag +gcacagaatttcctactgtaacgtgttttctcgatagaaacgtttctcca +aatcgaaatttttattagcaatcatcaattcgtcatgtttctgtgctgga +gcacattgttatgcagtgctcatgaatattcacagttgaaaatcgaattt +ttttttcttatttttattaacttctctcctcactcaagtgcaatctcatt +tcggcggaacgatgaaagcggactcgtttgaaacggattacactgctggc +tggctccatcttttttatttctggtttttttcccgacacgggaggtcatc +cgtccacgtcttcaatcttattcgcttctccttctatctatctctcttcc +aaaaaaatggaacagattgtccgccttctactttccgcatgcgcctattc +tagacatcgagaagaagcgagagaatccgaaaaactccgccgtccggcgc +ctagcgttcatcccgtcgcatccaatttccttcacccctgtctccagtct +ctaatctgtgtttcccagaccttctccttcttcttctcccctctttcttc +cctttcttttctacgattcctagacctgcccggttgaccatcgggcccac +catttatcgagcgcgtccgtctgttcgttgctgtgagcgcgcgcgcgcga +gcgcacactgcacaccatttgaccgcaacgagccgagagagtgtgtgaaa +tgaagagacgccgagtggacacgttgctctacaccaaacgcgctacacca +aatgggcggagacccaatggtgcaccaagtcagcagtataaaaggaatgg +aaatggtccattcagtcatcagttgtttttttattttctcttttctccca +tcactttctcccttcttcccctctcctaatttccattcccaactattatt +ctcggatcagatcgagccattgctggtttcttccacagtggtactttcca +ttagaactatcaccgggtggaaactagcagtggctcgatcttttccactt +gctccaccgctgtcggggaaccgcgccaattttcgcttcagtgctagacc +atccaaagtgtctatcaccgggtgaaaattcgcatgggtccccgacgcgg +aaagataaaatatcttaaaatcgattctagaaacccttggaccagtgtgg +gtgtccgttgcggtgctacattctctaatctgtatcaccgggtgaacact +tgcagtggtcctcgtggtttctctgtgagccaggtcctgttccggttttt +tccgtggtgataacgcatccaaaagtctctatcaccgggagaaaaactgg +agtaggacctgtgactcattccgatttctggagttttcccctacattcta +ccattcagctactgattattgaattcctgatataccgagagcccagctga +tttcgtcttggtaataagctcgtcattgagattatcaccgggtgtaaatc +agcttggctctggtgtctccgaacctcctgtccgcacctcagtggatgta +tgccatgatgataagatatcagaaatcctatcaccgggtgtacatcagct +aaggtgcgggtacaggtgcatttgatatcaaggtgagttatttttaagtg +ggtcccagagaccttggtggtttttctctgcagtgatagatacttctaac +aactcgctatcaccgggtgaaaaatcacctaggtctggagcctcctgctc +tttttttgctgtttttaaacttaaacttaaaactaacactttatcaaaat +aaagtcttccaaaatcttttttctgatctgccggaagactttccatgaat +ttgtccaaaactcgttgcactttatcctcgtcgtaatcatttgacaccat +atctttggataactagaataattgaacattggtttaaaaaaattctctca +aaaaaaaaatcacaaacctgatgaattttagcctcatctatagcagtatc +tgcgagaagaatcgtaagattcattgataattctatatattttccaataa +ttttatccgaagctggatgtgaagtttctacagtacctccgtggcataat +actacaatggaagcaaaaagagcgacaattaggatcgtcattttagtgga +gaatgatgaattgacccggctctttgggggttggaggattcattttcccc +ttcaacaggtgctcaaataattaaagagaatagaaccgacgatatatggg +tcaaatgtttatacagttgtgctactaaacgtattgttacacgcgttatt +aataattagaattagaattatatcgttttgtacggattgagaatcccatt +tgggtcgaaaatgttcttgagcttctttgtcaaaagtcgttcttcaggat +cttttccgaatgtggagtacggtagcttcagttgaccgattccatgttca +gctgaaattgacccgccgtgatcgacaacccattcgtagaggaagggata +gagcctggaatttgaaattattaatagaattaaaattttataaaaaagaa +aaatctcgaaacttacaatttttcaagttcttcattgtgtttttcagatg +taatatttaaatgagtgtttccatctcccaaatgtccataagtgacaatt +cttttagccaaagaaccacatcgttccttcatcacattcgtcaattcata +ataattttccaatggtaaagaaacatcatgcttatagacatatccatctc +tggtaaccgccaatggtgcactttctctcaattgccacatcttcgtagct +tctgcagaagatccagcgagcactccgtcgataatcagattttttgagag +gcattcatccaaaaatgcgctcattttctccatatcgtgatcttcattgg +atcctgatgtttcgacaaggatcgagaatggggttggagcattcagtact +gggtgcaatcctagattcgttttcaaacattccatcgtagcatcgtcgag +aagttcgaaggaggaaaggatttcagtgaggctggattttgcaagcttca +gtacttcgcagcattttttgaaggattcgatgcctgaaaaaaattagaaa +ttgaaaaatttgaacccattatataaatattcaacctaccaagcatcgca +ctttgtacacttttcggtttaggaaccgcagtcattgtgacgcttgtgat +aacacccaactgcccttcacttcccaagaataggtgtggagtgtgcaaag +ttgtgttgtccttccgaatgcttgatcccaaatgtagaacagttccatgt +tcatcgggaagaaccaccgtgagcccgagaagatgtgcgtgaagacttcc +gtatcgaatcaaccgaatccctcctgcacacgtggcaatatttcctccaa +tctgacaggatcctttggctccgagatcaaaaggcatcatatatccgagt +tttgcaagtttgttgtccaagtcttccagaataaaaccagaatcacactt +gagaattcccattgtgtcgtcgaaagagaattgcttgttgattttattca +ttgatataacaacttcatcatgtactggaattgatccaccaacgagtcct +gtattccctccttgtgggactactgccaatttgttcttggagcaatacgc +caatattgcagaaacctcttcggtgctcttcgggtagaggacgacactgc +caggacctggaaattaaaacatttaatatttaaagtacctatttaatatt +aaataaacctaatcttaaaatacaaatacctttaaattggcctgtccaat +ctgtagtatgatttgtaatatcgtccttcttcactgcatcttgcccgaga +aaattctcaaatgccattaaatccgactgcatcacttttgcaaatccttc +atgtctggcggcaagaactgctgcgtagcttctagttggtcttctgattc +gtggcaagattttcagaaacatctgaattcagaaacttttcaaaaaataa +cttgaaacttcaaaagaaatagtaggagacaaagctcggctaggtgaccg + +>chrIII:2172325-2172669 +CAGGCAGTCAGTCAGTCTCTCTCCACTCACATTCAGTCAGTCAGTGACCA +TCACCAGGTTGTGTGTGAGCCCCTTCCATTATTCTTCTGAACCCCCCTCC +CAACGCGGGAAGACTCGCCGGCAATGACACTGGTTATCTTTTCCATCGTG +GAATGCCCCCCATTGATTTTTTCCCCTTTTCGGGGGGAAAAAATTGGAAA +CGAGAAAGGTATCGGGTGTCATAGCCGGCGTGATCATCTTCCTCAAGTAT +TCCTCTGCTGATTTCGATATTCGGAGGAGCTCGGAGGCTGTTCAGCTGTA +AAATTGGTTGATTAAGCTCAAAAATCGGCGTTAACGCGGCTTTCC |
| b |
| diff -r 000000000000 -r af18bb0baa92 test-data/reads.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fa Tue Jan 27 09:06:06 2015 -0500 |
| b |
| b'@@ -0,0 +1,756666 @@\n+>nematode_1\n+TCACCGGGTGTAAATCAGCTTGTCGTATGCCGTCT\n+>nematode_2\n+TCACCGGGTGAACACTTGCAGTTCGTATGACGTCT\n+>nematode_3\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_4\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_5\n+TCACCGGGTGGAAACTAGCTGTCGTATGCCGTCTT\n+>nematode_6\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_7\n+TCACCGGGGGGAAACTAGCAGTTCGTATGCTGTTT\n+>nematode_8\n+TCACCGGGTGAACACCTGCAGTTCGTATGCCGTCT\n+>nematode_9\n+TCACCGGGCGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_10\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_11\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_12\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_13\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_14\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_15\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_16\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_17\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_18\n+TCACCGGGTGGAAACTAGCAGTCGTATGCCGTCAT\n+>nematode_19\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_20\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_21\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCTTCT\n+>nematode_22\n+TCACCGGGAGGAAACTAGCAGTCGTATGCCGTCTT\n+>nematode_23\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_24\n+TCACCGAGTGAACACTTGCATCGTATGCCGTCTTT\n+>nematode_25\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTC\n+>nematode_26\n+TCACCGGGTGGAAACTAGCAGTATCGTATGCCGTT\n+>nematode_27\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTTT\n+>nematode_28\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_29\n+TCACCGGGCGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_30\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_31\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_32\n+TCACCGGGTGGAAACTAGCAGATCGTATGCCGTCT\n+>nematode_33\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_34\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_35\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_36\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_37\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_38\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_39\n+AGCTGATTTCGTCTTGGTAATATCGTATGCCGTCT\n+>nematode_40\n+TCACCGGGTGGCAACTAGCAGTTCGTATTCCGTGT\n+>nematode_41\n+ACCGGGTGGAAACTAGCAGTTCGTATGCCGTCTTC\n+>nematode_42\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_43\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_44\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_45\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_46\n+TCACCGGGTGGAAACTATCAGTTCGTATGCCGTCT\n+>nematode_47\n+ACCGGGTGTACATCAGCTAATCGTATGCCGTCTTC\n+>nematode_48\n+TCACCGGGTGAACACTTGCAGTTTCGTATGCAGTC\n+>nematode_49\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_50\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_51\n+AGCTAATTTCGTCTTGGTAATATCGTATGCCGTCT\n+>nematode_52\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_53\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_54\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_55\n+TCACCGGGTGAAAATTCGCATGTCGTATGCCGTCT\n+>nematode_56\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_57\n+ACCGGGTGAACACTTGCAGTTCGTATGCCGTCTTT\n+>nematode_58\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_59\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_60\n+TCACCGGGTGGAAACTAGCAGTTTCGTATGCCGTT\n+>nematode_61\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_62\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_63\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_64\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_65\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_66\n+TCACCGGGTGGAAACTAGCATTTCGTATGCCGTCT\n+>nematode_67\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematode_68\n+TCACCGGGTGTACATCAGCTATCGTATGCCGTCTT\n+>nematode_69\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_70\n+TCACCGGGTGTAGATCAGCTAATCGTATGCTGTCT\n+>nematode_71\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_72\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_73\n+ACCGGGTGGAAACTAGCAGTCGTATGCCGTCTTCT\n+>nematode_74\n+TCACCGGGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_75\n+TCACCGCGTGGAAACTAGCAGTTCGTATGCCGTCT\n+>nematode_76\n+TCACCGGGTGAACACTTGCAGTTCGTATGCCGTCT\n+>nematode_77\n+TCACCGGGTGAACACTTGCAGTTCGTATGCAGTCT\n+>nematode_78\n+TCACCGGGTGTACATCAGCTAATCGTATGCCGTCT\n+>nematod'..b'GC\n+>nematode_378259\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378260\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378261\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378262\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378263\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378264\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378265\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378266\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378267\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378268\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378269\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378270\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378271\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378272\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378273\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378274\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378275\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378276\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378277\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378278\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378279\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378280\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378281\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378282\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378283\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378284\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378285\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378286\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378287\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378288\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378289\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378290\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378291\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378292\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378293\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378294\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378295\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378296\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378297\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378298\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378299\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378300\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378301\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378302\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378303\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378304\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378305\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378306\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378307\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378308\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378309\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378310\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378311\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378312\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378313\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378314\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378315\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378316\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378317\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378318\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378319\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378320\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378321\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378322\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378323\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378324\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378325\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378326\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378327\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378328\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378329\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378330\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378331\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n+>nematode_378332\n+AATGACACTGGTTATCTTTTCCATCGTCGTATGC\n' |
| b |
| diff -r 000000000000 -r af18bb0baa92 tool-data/bowtie_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie_indices.loc.sample Tue Jan 27 09:06:06 2015 -0500 |
| b |
| @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, +#then the bowtie_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie_indices.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r af18bb0baa92 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jan 27 09:06:06 2015 -0500 |
| 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> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r af18bb0baa92 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Jan 27 09:06:06 2015 -0500 |
| b |
| @@ -0,0 +1,65 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="perl" version="5.18.1"> + <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bowtie" version="0.12.7"> + <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="mirdeep2_mapper" version="2.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action> + <action type="move_file"> + <source>clip_adapters.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>collapse_reads_md.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>convert_bowtie_output.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>fastaparse.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>fastq2fasta.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>illumina_to_fasta.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>mapper.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>parse_mappings.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rna2dna.pl</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + +Processes reads and/or maps them to the reference genome. + +input: +Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used. +output: +The output depends on the options used (see below). Either a fasta file with processed reads or an arf file with with mapped reads, or both, are output. + + </readme> + </package> +</tool_dependency> |