Previous changeset 0:bee42f615f28 (2018-05-30) Next changeset 2:5c360c46eac7 (2018-06-05) |
Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit d3227eb74ad38fac307911b60c8a20a13349bcf9 |
modified:
macros.xml nanopolish_eventalign.xml |
added:
test-data/all_fasta.loc tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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diff -r bee42f615f28 -r c8c5caecfacc macros.xml --- a/macros.xml Wed May 30 11:55:18 2018 -0400 +++ b/macros.xml Tue Jun 05 17:53:36 2018 -0400 |
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@@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.9.0">nanopolish</requirement> + <requirement type="package" version="0.9.2">nanopolish</requirement> <yield/> </requirements> </xml> @@ -33,4 +33,4 @@ <yield /> </citations> </xml> -</macros> \ No newline at end of file +</macros> |
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diff -r bee42f615f28 -r c8c5caecfacc nanopolish_eventalign.xml --- a/nanopolish_eventalign.xml Wed May 30 11:55:18 2018 -0400 +++ b/nanopolish_eventalign.xml Tue Jun 05 17:53:36 2018 -0400 |
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@@ -17,12 +17,20 @@ nanopolish index -d fast5_files/ reads.fasta && ln -s '$b' reads.bam && ln -s '${b.metadata.bam_index}' reads.bam.bai && - ln -s '$g' genome.fa && + #if $reference_source.reference_source_selector == 'history': + ln -f -s '$reference_source.ref_file' genome.fa && + #else: + ln -f -s '$reference_source.ref_file.fields.path' genome.fa && + #end if nanopolish eventalign -r reads.fasta -b reads.bam -g genome.fa + #if str($min_mapping_quality): + -q $min_mapping_quality + #end if + --threads "\${GALAXY_SLOTS:-4}" $samples $scale_events $sam @@ -47,7 +55,22 @@ <!-- variants consensus inputs --> <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> - <param type="data" argument="-g" format="fasta" label="The reference genome"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> <!-- optional inputs --> <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true" @@ -56,6 +79,8 @@ <!-- optional params --> <param argument="-w" type="text" optional="true" label="find variants in window of region chromsome:start-end" /> + <param name="min_mapping_quality" type="integer" optional="true" value="" + label="Only use reads with mapping quality of at least this value" help="(-q)"/> <!-- optional flags --> <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true" @@ -74,37 +99,55 @@ <outputs> <!-- variants consensus outputs --> <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" /> - <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Computed variants"/> + <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Aligned squiggles"/> </outputs> <tests> <test> - <!-- index test --> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> - - <!-- variants consensus test --> <param name="b" value="reads.sorted.bam" /> - <param name="g" value="draft.fa" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-200010" /> <param name="sam" value="true" /> - <output name="output_summary" file="eventalign-summary.txt" /> <output name="output_eventalign" file="reads-draft.eventalign.sam"/> </test> <test> - <!-- index test --> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> - - <!-- variants consensus test --> <param name="b" value="reads.sorted.bam" /> - <param name="g" value="draft.fa" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-200010" /> <param name="sam" value="false" /> <param name="summary" value="false" /> <param name="scale_events" value="true" /> <param name="print_read_names" value="true" /> - + <param name="min_mapping_quality" value="0" /> + <output name="output_summary" file="t2-eventalign-summary.txt" /> + <output name="output_eventalign"> + <assert_contents> + <has_text text="contig" /> + <has_text text="position" /> + <has_text text="event_index" /> + <has_text text="tig00000001" /> + </assert_contents> + </output> + </test> + <test> + <!-- test data table reference --> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + <param name="b" value="reads.sorted.bam" /> + <param name="reference_source_selector" value="cached" /> + <param name="ref_file" value="draft"/> + <param name="w" value="tig00000001:200000-200010" /> + <param name="sam" value="false" /> + <param name="summary" value="false" /> + <param name="scale_events" value="true" /> + <param name="print_read_names" value="true" /> + <param name="min_mapping_quality" value="0" /> <output name="output_summary" file="t2-eventalign-summary.txt" /> <output name="output_eventalign"> <assert_contents> |
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diff -r bee42f615f28 -r c8c5caecfacc test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Tue Jun 05 17:53:36 2018 -0400 |
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@@ -0,0 +1,1 @@ +draft draft draft ${__HERE__}/draft.fa \ No newline at end of file |
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diff -r bee42f615f28 -r c8c5caecfacc tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jun 05 17:53:36 2018 -0400 |
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@@ -0,0 +1,9 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables> + |
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diff -r bee42f615f28 -r c8c5caecfacc tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Jun 05 17:53:36 2018 -0400 |
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@@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |