# HG changeset patch
# User diodupima
# Date 1625674780 0
# Node ID 88fe28c4976de5235a0013e19114f9c421db7420

"planemo upload commit 4ee329c2779b2e6e1ea0b58e4c636ff0658a8852-dirty"

diff -r 000000000000 -r 88fe28c4976d coast_search_blast.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coast_search_blast.xml	Wed Jul 07 16:19:40 2021 +0000
@@ -0,0 +1,46 @@
+<tool id="coast_search_blast" name="COAST - Search with BLAST" version="0.1.1">
+    <description>Run a new job, and identify the closest proteomes, using BLAST</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="2.10">blast</requirement>
+        <expand macro="requirements"/>
+    </requirements>
+    <command ><![CDATA[
+        coast
+        @QUERY@
+        @DB@
+        --engine blast
+        --inplace_workspace
+        @AAI_FILTER@
+        @OUTPUT@
+        @QUERY_KEYWORDS@
+        @OUTPUT_FORMAT@
+        @BLAST_TAX_FILTER@
+        @BLAST_ALN_OPTIONS@
+        @GENERIC_ALN_OPTIONS@
+    ]]></command>
+    <inputs>
+        <expand macro="input_query" />
+        <expand macro="protein_db" />
+        <expand macro="blast_taxon_filter"/>
+        <expand macro="output_format"/>
+        <expand macro="aai_filter"/>
+        <section name="aln_adv" title="Advanced Alignment Settings" >
+            <expand macro="blast_aln_options"/>
+            <expand macro="generic_aln_options"/>
+        </section>
+    </inputs>
+    <outputs>
+        <expand macro="results_alignment"/>
+        <expand macro="results_report"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    COAST BLASTp
+        Alignment search tool that identifies similar proteomes using the BLASTp alignment engine.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 88fe28c4976d macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Jul 07 16:19:40 2021 +0000
@@ -0,0 +1,228 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.1</token>
+    <xml name="requirements">
+        <requirement type="package" version="0.1.1">coast</requirement>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@misc{noauthor_coast_nodate,
+                    title = {{COAST} - {Compartive} {Ominc} {Alignment} {Search} {Tool}},
+                    url = {https://gitlab.com/coast_tool/COAST},
+                    abstract = {Alignment search tool that identifies similar proteomes},
+                    language = {en},
+                    urldate = {2021-06-22},
+                }
+            </citation>
+        </citations>
+    </xml>
+    <xml name="input_query">
+        <conditional name="query_type">
+            <param name="source" type="select" label="Select the type of input file">
+                <option value="coast_gb">COAST from GenBank</option>
+                <option value="coast_fa">COAST from FASTA</option>
+            </param>
+            <when value="coast_gb">
+                <param name="query_file" type="data" format="GenBank" label="Load a query proteome in Genebank"/>
+                <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.">
+                    <option value="CDS" selected="true">CDS</option>
+                    <option value="product">product</option>
+                </param>
+            </when>
+            <when value="coast_fa">
+                <param name="query_file" type="data" format="FASTA" label="Load a query proteome in FASTA"/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@QUERY@"><![CDATA[
+        "$query_type.query_file"
+    ]]></token>
+    <token name="@QUERY_KEYWORDS@"><![CDATA[
+        #if $query_type.source == 'coast_gb'
+            --keywords '$query_type.query_key'
+        #end if
+    ]]></token>
+
+    <xml name="protein_db">
+        <param name="db" type="select" optional="false" label="BLAST-Ready protein sequences database.">
+            <options from_data_table="blastdb_p" />
+        </param>
+    </xml>
+    <token name="@DB@"><![CDATA[
+        "$db"
+    ]]></token>
+
+    <xml name="output_format">
+        <param name="outfmt" type="select" optional="true" multiple="true" display="checkboxes" label="Select outputs">
+            <option value="b" selected="true">Best Hits</option>
+            <option value="a" selected="true">Aggregated Metrics</option>
+            <option value="r" selected="true">Report</option>
+        </param>
+    </xml>
+    <token name="@OUTPUT_FORMAT@"><![CDATA[
+        #if $outfmt
+            --outfmt
+            #for $format in $outfmt
+                '${format}'
+            #end for
+        #end if
+    ]]></token>
+    <token name="@OUTPUT@"><![CDATA[
+        --quiet
+    ]]></token>
+
+    <xml name="aai_filter">
+        <param name="aai" type="integer" value="10" label="AAIc filtering score"/>
+        <param name="min_cov" type="integer" value="50" label="Minimum Coverage for AAIbd hit selection"/>
+        <param name="min_id" type="integer" value="40" label="Minimum Amino Acid Identity for AAIbd hit selection"/>
+    </xml>
+    <token name="@AAI_FILTER@"><![CDATA[
+        --aai '$aai'
+        --cov '$min_cov'
+        --id '$min_id'
+    ]]></token>
+
+    <xml name="hypothetical_filter">
+        <param name="hypothetical" type="boolean" checked="false" label="Filter hypothetical proteins from query. Read description for more information." truevalue="--filter_hypothetical" falsevalue=""/>
+    </xml>
+    <token name="@HYPO_FILTER@"><![CDATA[
+        #if $hypothetical
+            '$hypothetical'
+        #end if
+    ]]></token>
+
+    <xml name="results_alignment">
+        <data format_source="tabular" format="tabular" name="blast_results" label="COAST - Batch alignment results" from_work_dir="blast_results.tab"/>
+    </xml>
+
+    <xml name="results_report">
+        <data format_source="html"  format="html" name="coast_report" label="COAST - Summarized report" from_work_dir="coast_report.html">
+            <filter>"r" in outfmt</filter>
+        </data>
+        <data format_source="tabular" format="tabular" label="COAST - Best-hits table" name="bh_results" from_work_dir="bh_results.tab">
+            <filter>"b" in outfmt</filter>
+        </data>
+        <data format_source="tabular" format="tabular" label="COAST - Results table" name="coast_results" from_work_dir="coast_results.tab">
+            <filter>"a" in outfmt</filter>
+        </data>
+    </xml>
+
+    <xml name="blast_taxon_filter">
+        <conditional name="filter_type">
+            <param name="taxon_filter_type" type="select" label="Type of taxonomic filter">
+                <option value="taxidlist_dm">Pre-defined taxonomic filters</option>
+                <option value="taxidlist_user">User-provided file based list</option>
+                <option value="taxonlist">Comma separated list</option>
+            </param>
+            <when value="taxidlist_dm">
+                <param name="taxidlist" type="select" optional="true" label="Select pre-defined taxonomic filters">
+                    <options from_data_table="coast_taxonomic_filters" />
+                </param>
+            </when>
+            <when value="taxidlist_user">
+                <param name="taxidlist" type="data" format="txt" optional="true" label="Load file with filtering taxids."/>
+            </when>
+            <when value="taxonlist">
+                <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@BLAST_TAX_FILTER@"><![CDATA[
+        #if $filter_type.taxon_filter_type == "taxidlist_dm"
+            --taxidlist '$filter_type.taxidlist.fields.path'
+        #end if
+        #if $filter_type.taxon_filter_type == "taxidlist_user"
+            --taxidlist '$filter_type.taxidlist'
+        #end if
+        #if $filter_type.taxon_filter_type == "taxonlist"
+            --taxonlist '$filter_type.taxonlist'
+        #end if
+    ]]></token>
+
+    <xml name="diamond_taxon_filter">
+        <conditional name="filter_type">
+            <param name="taxon_filter_type" type="select" label="Type of taxonomic filter">
+                <option value="taxonlist_pre_defined">Pre-defined taxonomic filters</option>
+                <option value="taxonlist">Comma separated list</option>
+            </param>
+        <when value="taxonlist_pre_defined">
+            <param name="taxonlist" type="select" optional="true" label="Select pre-defined taxonomic filters">
+                <option value="10239">Viruses - 102239</option>
+                <option value="2157">Archaea - 2157</option>
+                <option value="2">Bacteria - 2</option>
+            </param>
+        </when>
+        <when value="taxonlist">
+            <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/>
+        </when>
+        </conditional>
+    </xml>
+    <token name="@DIAMOND_TAX_FILTER@"><![CDATA[
+        #if $taxonlist
+            --taxonlist '$taxonlist'
+        #end if
+    ]]></token>
+
+    <xml name="generic_aln_options">
+        <param name="threshold_no" type="integer" optional="true" label="E-Value Threshold"/>
+        <param name="scoring_matrix" type="select" optional="true" label="Scoring matrix">
+            <option value="BLOSUM45">BLOSUM45</option>
+            <option value="BLOSUM50">BLOSUM50</option>
+            <option value="BLOSUM62">BLOSUM62</option>
+            <option value="BLOSUM80">BLOSUM80</option>
+            <option value="BLOSUM90">BLOSUM90</option>
+            <option value="PAM250">PAM250</option>
+            <option value="PAM70">PAM70</option>
+            <option value="PAM30">PAM30</option>
+        </param>
+        <param name="gap_open" type="integer" optional="true" label="Gap opening penalty"/>
+        <param name="gap_ext" type="integer" optional="true" label="Gap extension penalty"/>
+    </xml>
+    <token name="@GENERIC_ALN_OPTIONS@"><![CDATA[
+        #if $aln_adv.scoring_matrix
+            --matrix '$aln_adv.scoring_matrix'
+        #end if
+        #if $aln_adv.threshold_no
+            --evalue '$aln_adv.threshold_no'
+        #end if
+        #if $aln_adv.gap_open
+            --gapopen '$aln_adv.gap_open'
+        #end if
+        #if $aln_adv.gap_ext
+            --gapextend '$aln_adv.gap_ext'
+        #end if
+    ]]></token>
+
+    <xml name="blast_aln_options">
+        <param name="task" type="select" optional="true" label="Type of BLAST">
+            <option value="blast">blast</option>
+            <option value="blastp-fast">blastp-fast</option>
+            <option value="blastp-short">blastp-short</option>
+        </param>
+    </xml>
+    <token name="@BLAST_ALN_OPTIONS@"><![CDATA[
+        #if $aln_adv.task
+            --task '$aln_adv.task'
+        #end if
+    ]]></token>
+
+    <xml name="diamond_aln_options">
+        <param name="diamond_sens" type="select" label="Select the desired sensibility">
+            <option value="sensitive" selected="true">sensitive</option>
+            <option value="more-sensitive">more sensitive</option>
+            <option value="very-sensitive">very sensitive</option>
+            <option value="ultra-sensitive">ultra sensitive</option>
+        </param>
+    </xml>
+    <token name="@DIAMOND_ALN_OPTIONS@"><![CDATA[
+        #if $aln_adv.diamond_sens
+            --sens '$aln_adv.diamond_sens'
+        #end if
+    ]]></token>
+
+    <xml name="merlin_db_selection">
+        <param name="db" type="select" label="Select the desired database">
+            <option value="UniProtKB_SwissProt">SwissProt</option>
+            <option value="UniProtKB_Trembl">Trembl</option>
+        </param>
+    </xml>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r 88fe28c4976d 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 16:19:40 2021 +0000
@@ -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
diff -r 000000000000 -r 88fe28c4976d 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 16:19:40 2021 +0000
@@ -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