| Next changeset 1:b9ce87709188 (2021-07-07) |
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Commit message:
"planemo upload commit 4ee329c2779b2e6e1ea0b58e4c636ff0658a8852-dirty" |
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added:
coast_report.xml macros.xml table_data_table_conf.xml.sample tool-data/coast_taxonomic_filters.loc.sample |
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| diff -r 000000000000 -r a3b2bcd29c39 coast_report.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/coast_report.xml Wed Jul 07 16:20:26 2021 +0000 |
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| @@ -0,0 +1,41 @@ +<tool id="coast_report" name="COAST - Report generator" version="0.1.1"> + <description>Recreate the report and outputs with different settings</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="requirements"/> + </requirements> + <command><![CDATA[ + coast_report + @QUERY@ + "$result_file" + @AAI_FILTER@ + @HYPO_FILTER@ + @OUTPUT@ + @QUERY_KEYWORDS@ + @OUTPUT_FORMAT@ + ]]></command> + <inputs> +<!--Select the kind of input to be used--> + <expand macro="input_query" /> + <param name="result_file" type="data" format="tabular" label="Load previous COAST generated alignment file"/> +<!--Outputs selection--> + <expand macro="output_format"/> +<!--AAI filtering score--> + <expand macro="aai_filter"/> + <expand macro="hypothetical_filter"/> + </inputs> + <outputs> + <expand macro="results_report"/> + </outputs> + <tests> + <test> + </test> + </tests> + <help><![CDATA[ + COAST Report + Generate COAST reports and outputs based in different parameters. + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r a3b2bcd29c39 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 07 16:20:26 2021 +0000 |
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| b'@@ -0,0 +1,228 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">0.1.1</token>\n+ <xml name="requirements">\n+ <requirement type="package" version="0.1.1">coast</requirement>\n+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="bibtex">@misc{noauthor_coast_nodate,\n+ title = {{COAST} - {Compartive} {Ominc} {Alignment} {Search} {Tool}},\n+ url = {https://gitlab.com/coast_tool/COAST},\n+ abstract = {Alignment search tool that identifies similar proteomes},\n+ language = {en},\n+ urldate = {2021-06-22},\n+ }\n+ </citation>\n+ </citations>\n+ </xml>\n+ <xml name="input_query">\n+ <conditional name="query_type">\n+ <param name="source" type="select" label="Select the type of input file">\n+ <option value="coast_gb">COAST from GenBank</option>\n+ <option value="coast_fa">COAST from FASTA</option>\n+ </param>\n+ <when value="coast_gb">\n+ <param name="query_file" type="data" format="GenBank" label="Load a query proteome in Genebank"/>\n+ <param name="query_key" type="select" label="List the GB file Features to be used as Proteins, do so in a way to prevent duplicated proteins.">\n+ <option value="CDS" selected="true">CDS</option>\n+ <option value="product">product</option>\n+ </param>\n+ </when>\n+ <when value="coast_fa">\n+ <param name="query_file" type="data" format="FASTA" label="Load a query proteome in FASTA"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@QUERY@"><![CDATA[\n+ "$query_type.query_file"\n+ ]]></token>\n+ <token name="@QUERY_KEYWORDS@"><![CDATA[\n+ #if $query_type.source == \'coast_gb\'\n+ --keywords \'$query_type.query_key\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="protein_db">\n+ <param name="db" type="select" optional="false" label="BLAST-Ready protein sequences database.">\n+ <options from_data_table="blastdb_p" />\n+ </param>\n+ </xml>\n+ <token name="@DB@"><![CDATA[\n+ "$db"\n+ ]]></token>\n+\n+ <xml name="output_format">\n+ <param name="outfmt" type="select" optional="true" multiple="true" display="checkboxes" label="Select outputs">\n+ <option value="b" selected="true">Best Hits</option>\n+ <option value="a" selected="true">Aggregated Metrics</option>\n+ <option value="r" selected="true">Report</option>\n+ </param>\n+ </xml>\n+ <token name="@OUTPUT_FORMAT@"><![CDATA[\n+ #if $outfmt\n+ --outfmt\n+ #for $format in $outfmt\n+ \'${format}\'\n+ #end for\n+ #end if\n+ ]]></token>\n+ <token name="@OUTPUT@"><![CDATA[\n+ --quiet\n+ ]]></token>\n+\n+ <xml name="aai_filter">\n+ <param name="aai" type="integer" value="10" label="AAIc filtering score"/>\n+ <param name="min_cov" type="integer" value="50" label="Minimum Coverage for AAIbd hit selection"/>\n+ <param name="min_id" type="integer" value="40" label="Minimum Amino Acid Identity for AAIbd hit selection"/>\n+ </xml>\n+ <token name="@AAI_FILTER@"><![CDATA[\n+ --aai \'$aai\'\n+ --cov \'$min_cov\'\n+ --id \'$min_id\'\n+ ]]></token>\n+\n+ <xml name="hypothetical_filter">\n+ <param name="hypothetical" type="boolean" checked="false" label="Filter hypothetical proteins from query. Read description for more information." truevalue="--filter_hypothetical" falsevalue=""/>\n+ </xml>\n+ <token name="@HYPO_FILTER@"><![CDATA[\n+ #if $hypothetical\n+ \'$hypothetical\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="results_alignment">\n+ <data format_source="tabular" format="tabular" name="blast_results" label="COAST - Batch alignment results" from_work_dir="blast_'..b'st\'\n+ #end if\n+ #if $filter_type.taxon_filter_type == "taxonlist"\n+ --taxonlist \'$filter_type.taxonlist\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="diamond_taxon_filter">\n+ <conditional name="filter_type">\n+ <param name="taxon_filter_type" type="select" label="Type of taxonomic filter">\n+ <option value="taxonlist_pre_defined">Pre-defined taxonomic filters</option>\n+ <option value="taxonlist">Comma separated list</option>\n+ </param>\n+ <when value="taxonlist_pre_defined">\n+ <param name="taxonlist" type="select" optional="true" label="Select pre-defined taxonomic filters">\n+ <option value="10239">Viruses - 102239</option>\n+ <option value="2157">Archaea - 2157</option>\n+ <option value="2">Bacteria - 2</option>\n+ </param>\n+ </when>\n+ <when value="taxonlist">\n+ <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <token name="@DIAMOND_TAX_FILTER@"><![CDATA[\n+ #if $taxonlist\n+ --taxonlist \'$taxonlist\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="generic_aln_options">\n+ <param name="threshold_no" type="integer" optional="true" label="E-Value Threshold"/>\n+ <param name="scoring_matrix" type="select" optional="true" label="Scoring matrix">\n+ <option value="BLOSUM45">BLOSUM45</option>\n+ <option value="BLOSUM50">BLOSUM50</option>\n+ <option value="BLOSUM62">BLOSUM62</option>\n+ <option value="BLOSUM80">BLOSUM80</option>\n+ <option value="BLOSUM90">BLOSUM90</option>\n+ <option value="PAM250">PAM250</option>\n+ <option value="PAM70">PAM70</option>\n+ <option value="PAM30">PAM30</option>\n+ </param>\n+ <param name="gap_open" type="integer" optional="true" label="Gap opening penalty"/>\n+ <param name="gap_ext" type="integer" optional="true" label="Gap extension penalty"/>\n+ </xml>\n+ <token name="@GENERIC_ALN_OPTIONS@"><![CDATA[\n+ #if $aln_adv.scoring_matrix\n+ --matrix \'$aln_adv.scoring_matrix\'\n+ #end if\n+ #if $aln_adv.threshold_no\n+ --evalue \'$aln_adv.threshold_no\'\n+ #end if\n+ #if $aln_adv.gap_open\n+ --gapopen \'$aln_adv.gap_open\'\n+ #end if\n+ #if $aln_adv.gap_ext\n+ --gapextend \'$aln_adv.gap_ext\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="blast_aln_options">\n+ <param name="task" type="select" optional="true" label="Type of BLAST">\n+ <option value="blast">blast</option>\n+ <option value="blastp-fast">blastp-fast</option>\n+ <option value="blastp-short">blastp-short</option>\n+ </param>\n+ </xml>\n+ <token name="@BLAST_ALN_OPTIONS@"><![CDATA[\n+ #if $aln_adv.task\n+ --task \'$aln_adv.task\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="diamond_aln_options">\n+ <param name="diamond_sens" type="select" label="Select the desired sensibility">\n+ <option value="sensitive" selected="true">sensitive</option>\n+ <option value="more-sensitive">more sensitive</option>\n+ <option value="very-sensitive">very sensitive</option>\n+ <option value="ultra-sensitive">ultra sensitive</option>\n+ </param>\n+ </xml>\n+ <token name="@DIAMOND_ALN_OPTIONS@"><![CDATA[\n+ #if $aln_adv.diamond_sens\n+ --sens \'$aln_adv.diamond_sens\'\n+ #end if\n+ ]]></token>\n+\n+ <xml name="merlin_db_selection">\n+ <param name="db" type="select" label="Select the desired database">\n+ <option value="UniProtKB_SwissProt">SwissProt</option>\n+ <option value="UniProtKB_Trembl">Trembl</option>\n+ </param>\n+ </xml>\n+</macros>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r a3b2bcd29c39 table_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/table_data_table_conf.xml.sample Wed Jul 07 16:20:26 2021 +0000 |
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| @@ -0,0 +1,7 @@ +<!-- 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> + <table name="coast_taxonomic_filters" comment_char="#" allow_duplicate_entries="False"> + <columns>value, name, node_name, path</columns> + <file path="tool-data/coast_taxonomic_filters.loc" /> + </table> +</tables> \ No newline at end of file |
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| diff -r 000000000000 -r a3b2bcd29c39 tool-data/coast_taxonomic_filters.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/coast_taxonomic_filters.loc.sample Wed Jul 07 16:20:26 2021 +0000 |
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| @@ -0,0 +1,28 @@ +#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 sam_fa_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc +#file has this format (white space characters are TAB characters): +# +#index <seq> <location> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/sam/, +#then the sam_fa_indices.loc entry would look like this: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +# +#and your /depot/data2/galaxy/sam/ directory +#would contain hg18.fa and hg18.fa.fai files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai +# +#Your coast_taxonomic_filters.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: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa \ No newline at end of file |