--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/taxonomy_wf.xml	Fri Jul 29 20:32:07 2022 +0000
@@ -0,0 +1,227 @@
+<tool id="checkm_taxonomy_wf" name="CheckM taxonomy_wf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Analyze all genome bins with the same marker set
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+@BIN_INPUTS@
+
+checkm taxonomy_wf
+    '$rank_taxon.rank'
+    '$rank_taxon.taxon.fields.value'
+    'bins'
+    'output'
+    $analyze.ali
+    $analyze.nt
+    $analyze.genes
+    $qa.individual_markers
+    $qa.skip_adj_correction
+    $qa.skip_pseudogene_correction
+    --aai_strain $qa.aai_strain
+    $qa.ignore_thresholds
+    --e_value $qa.e_value
+    --length $qa.length
+    --file '$results'
+    --tab_table
+    --extension 'fasta'
+    --threads \${GALAXY_SLOTS:-1}
+    ]]></command>
+    <inputs>
+        <expand macro="rank_taxon"/>
+        <expand macro="bin_inputs"/>
+        <section name="analyze" title="Marker gene identification">
+            <expand macro="analyze_params" />
+        </section>
+        <section name="qa" title="Bin assessment">
+            <expand macro="qa_params" />
+        </section>
+        <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
+            <option value="marker_file">Marker genes</option>
+            <option value="hmmer_analyze">Marker gene HMM hits to each bin</option>
+            <option value="bin_stats_analyze">Marker gene bin stats</option>
+            <option value="checkm_hmm_info">Marker gene HMM info for each bin</option>
+            <expand macro="analyze_extra_output_options" />
+            <option value="bin_stats_ext">Marker gene bin extensive stats</option>
+            <expand macro="qa_extra_output_options" />
+        </param>
+    </inputs>
+    <outputs>
+        <data name="results" format="tabular" label="${tool.name} on ${on_string}: Bin statistics"/>
+        <!-- taxon_set outputs -->
+        <data name="marker_file" format="tabular" from_work_dir="output/*.ms" label="${tool.name} on ${on_string}: Marker genes">
+            <filter>'marker_file' in extra_outputs</filter>
+        </data>
+        <!--analyze outputs-->
+        <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
+            <filter>'hmmer_analyze' in extra_outputs</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats">
+            <filter>'bin_stats_analyze' in extra_outputs</filter>
+        </data>
+        <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" >
+            <filter>'checkm_hmm_info' in extra_outputs</filter>
+        </data>
+        <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
+            <filter>analyze['ali'] and 'hmmer_analyze_ali' in extra_outputs</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <!--qa outputs-->
+        <data name="bin_stats_ext" format="tabular" from_work_dir="output/storage/bin_stats_ext.tsv" label="${tool.name} on ${on_string}: Marker gene bin extensive stats">
+            <filter>'bin_stats_ext' in extra_outputs</filter>
+        </data>
+        <expand macro="qa_extra_outputs" />
+        <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv"  label="${tool.name} on ${on_string}: Marker gene statistics">
+            <filter>'marker_gene_stats' in extra_outputs</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="bins">
+                <param name="select" value="collection"/>
+                <param name="bins_coll">
+                    <collection type="list">
+                        <element name="637000110" ftype="fasta" value="637000110.fna"/>
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="rank_taxon">
+                <param name="rank" value="life"/>
+                <param name="taxon" value="Prokaryote"/>
+            </conditional>
+            <section name="analyze">
+                <param name="ali" value="false"/>
+                <param name="nt" value="false"/>
+                <param name="genes" value="false"/>
+            </section>
+            <section name="qa">
+                <param name="individual_markers" value="false"/>
+                <param name="skip_adj_correction" value="false"/>
+                <param name="skip_pseudogene_correction" value="false"/>
+                <param name="aai_strain" value="0.9"/>
+                <param name="ignore_thresholds" value="false"/>
+                <param name="e_value" value="1e-10"/>
+                <param name="length" value="0.7"/>
+            </section>
+            <param name="extra_outputs" value=""/>
+            <output name="results" ftype="tabular">
+                <assert_contents>
+                    <has_text text="637000110"/>
+                    <has_text text="Marker lineage"/>
+                    <has_text text="Prokaryote"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="8">
+            <conditional name="bins">
+                <param name="select" value="collection"/>
+                <param name="bins_coll">
+                    <collection type="list">
+                        <element name="637000110" ftype="fasta" value="637000110.fna"/>
+                    </collection>
+                </param>
+            </conditional>
+            <conditional name="rank_taxon">
+                <param name="rank" value="life"/>
+                <param name="taxon" value="Prokaryote"/>
+            </conditional>
+            <section name="analyze">
+                <param name="ali" value="true"/>
+                <param name="nt" value="false"/>
+                <param name="genes" value="false"/>
+            </section>
+            <section name="qa">
+                <param name="individual_markers" value="false"/>
+                <param name="skip_adj_correction" value="false"/>
+                <param name="skip_pseudogene_correction" value="false"/>
+                <param name="aai_strain" value="0.9"/>
+                <param name="ignore_thresholds" value="false"/>
+                <param name="e_value" value="1e-10"/>
+                <param name="length" value="0.7"/>
+            </section>
+            <param name="extra_outputs" value="marker_file,hmmer_analyze,hmmer_analyze_ali,bin_stats_analyze,bin_stats_ext,checkm_hmm_info,marker_gene_stats"/>
+            <output name="results" ftype="tabular">
+                <assert_contents>
+                    <has_text text="637000110"/>
+                    <has_text text="Marker lineage"/>
+                    <has_text text="Prokaryote"/>
+                </assert_contents>
+            </output>
+            <output name="marker_file" ftype="tabular">
+                <assert_contents>
+                    <has_text text="[Taxon Marker File]"/>
+                    <has_text text="Prokaryote"/>
+                    <has_text text="PF01000.21"/>
+                </assert_contents>
+            </output>
+            <output_collection name="hmmer_analyze" count="1">
+                <element name="637000110" ftype="txt">
+                    <assert_contents>
+                        <has_text text="target name"/>
+                        <has_text text="AC_000091_570"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="bin_stats_analyze" ftype="tabular">
+                <assert_contents>
+                    <has_text text="637000110"/>
+                    <has_text text="GC"/>
+                    <has_text text="GC std"/>
+                </assert_contents>
+            </output>
+            <output name="checkm_hmm_info" ftype="zip">
+                <assert_contents>
+                    <has_size value="4373" delta="100"/>
+                </assert_contents>
+            </output>
+            <output_collection name="hmmer_analyze_ali" count="1">
+                <element name="637000110" ftype="txt">
+                    <assert_contents>
+                        <has_text text="hmmsearch"/>
+                        <has_text text="Query"/>
+                        <has_text text="TOBE_2"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output name="bin_stats_ext" ftype="tabular">
+                <assert_contents>
+                    <has_text text="637000110"/>
+                    <has_text text="marker lineage"/>
+                </assert_contents>
+            </output>
+            <output name="marker_gene_stats" ftype="tabular">
+                <assert_contents>
+                    <has_text text="637000110"/>
+                    <has_text text="AC_000091_79"/>
+                    <has_text text="PF00318.15"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This command runs recommended workflow to analyze all genome bins with the same marker set. A common example would be a set of genomes from the same taxonomic group. 
+
+The workflow for using a taxonomic-specific marker set consists of 3 mandatory (M) steps and 1 recommended (R) step:
+
+- (R) The taxon_list command produces a table indicating all taxa for which a marker set can be produced. All support taxa at a given taxonomic rank can be produced by passing taxon_list the --rank flag
+- (M) The taxon_set command is used to produce marker sets for a specific taxon:
+- (M) The analyze command identifies marker genes within each genome bin and estimate completeness and contamination. All putative genomes to be analyzed must be provided.
+- (M) The qa command is used to produce different tables summarizing the quality of each genome bin.
+
+Inputs
+======
+
+
+Outputs
+=======
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>