--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/analyze.xml	Fri Jul 29 20:31:27 2022 +0000
@@ -0,0 +1,130 @@
+<tool id="checkm_analyze" name="CheckM analyze" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Identify marker genes in bins and calculate genome statistics
+    </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 analyze
+    '$marker_file'
+    'bins'
+    'output'
+    $ali
+    $nt
+    $genes
+    --extension 'fasta'
+    --threads \${GALAXY_SLOTS:-1}
+    ]]></command>
+    <inputs>
+        <expand macro="bin_inputs" />
+        <expand macro="marker_file" />
+        <expand macro="analyze_params"/>
+        <param name="extra_outputs" type="select" multiple="true" optional="true" label="Extra outputs">
+            <expand macro="analyze_extra_output_options" />
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="hmmer_analyze" type="list" label="${tool.name} on ${on_string}: Marker gene HMM hits to each bin">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.analyze\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
+        </collection>
+        <data name="bin_stats_analyze" format="tabular" from_work_dir="output/storage/bin_stats.analyze.tsv" label="${tool.name} on ${on_string}: Marker gene bin stats" />
+        <data name="checkm_hmm_info" format="zip" from_work_dir="output/storage/checkm_hmm_info.pkl.gz" label="${tool.name} on ${on_string}: Marker gene HMM info for each bin" />
+        <collection name="hmmer_analyze_ali" type="list" label="${tool.name} on ${on_string}: HMMER alignment file for each bin">
+            <filter>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>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="3">
+            <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>
+            <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
+            <param name="ali" value="false"/>
+            <param name="nt" value="false"/>
+            <param name="genes" value="false"/>
+            <param name="extra_outputs" value=""/>
+            <output_collection name="hmmer_analyze" count="1">
+                <element name="637000110" ftype="txt">
+                    <assert_contents>
+                        <has_text text="target name"/>
+                        <has_text text="AC_000091_859"/>
+                    </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="99600" delta="500"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="4">
+            <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>
+            <param name="marker_file" ftype="tabular" value="lineage_marker_set"/>
+            <param name="ali" value="true"/>
+            <param name="nt" value="true"/>
+            <param name="genes" value="false"/>
+            <param name="extra_outputs" value="hmmer_analyze_ali"/>
+            <output_collection name="hmmer_analyze" count="1">
+                <element name="637000110" ftype="txt">
+                    <assert_contents>
+                        <has_text text="target name"/>
+                        <has_text text="AC_000091_859"/>
+                    </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="99600" delta="500"/>
+                </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="ACCA"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This command identifies marker genes in bins and calculates genome statistics
+    ]]></help>
+    <expand macro="citations"/>
+</tool>