--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/place_seqs.xml	Sat Mar 04 20:25:10 2023 +0000
@@ -0,0 +1,132 @@
+<tool id="picrust2_place_seqs" name="PICRUSt2 Sequence placement" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>into reference tree</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tool"/>
+    <expand macro="requirements"/>
+    <version_command>place_seqs.py -v</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+@VAR_ACCESS_FOO@
+@PLACE_SEQS_PREPROCESSING@
+
+#if $intermediate_check
+    mkdir intermediate &&
+#end if
+
+place_seqs.py
+    @PLACE_SEQS_PARAMS@
+    --out_tree '$out_tree'
+    --processes "\${GALAXY_SLOTS:-1}"
+#if $intermediate_check
+    --intermediate 'intermediate/place_seqs'
+#end if
+## not implemented --chunk_size hoping that the default is carefully chosen
+## otherwise one might need to compute a "good" value from the input size
+## and the number of available processors
+    ]]></command>
+    <inputs>
+        <expand macro="place_seqs_params"/>
+        <param argument="--intermediate_check" type="boolean" truevalue="intermediate_check" falsevalue="" checked="false" label="Keep intermediate files" help="Intermediate output files will be deleted by default"/>
+   </inputs>
+   <outputs>
+        <expand macro="place_seqs_output" from_work_dir="./">
+            <filter>intermediate_check is True</filter>
+        </expand>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="study_fasta" ftype="fasta" value="study_seqs_test.fasta"/>
+            <param name="placement_tool" value="sepp"/>
+            <param name="intermediate_check" value="true"/>
+            <param name="min_align" value="0.80"/>
+            <output name="out_tree" ftype="newick">
+                <assert_contents>
+                    <has_text text="643348582"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+            <output_collection name="place_seqs_intermediate_output" type="list" count="2">
+                <element name="query_align" ftype="stockholm">
+                    <assert_contents>
+                        <has_text text="STOCKHOLM 1.0"/>
+                        <has_n_lines n="160106"/>
+                    </assert_contents>
+                </element>
+                <element name="study_seqs_filtered" ftype="fasta">
+                    <assert_contents>
+                        <has_text text="02905cfb87861c837dde629596d9272b"/>
+                        <has_n_lines n="10"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <assert_command>
+                <!-- make sure that prokaryotic reference is implemented by not
+                     setting the ref_dir parameter, i.e. use the programms default -->
+                <has_text text="prokaryotic/pro_ref/" negate="true"/>
+                <has_text text="--ref_dir" negate="true"/>
+            </assert_command>
+        </test>
+        <!-- input data does not really work with fungal reference - but sufficient for CLI test -->
+        <test expect_num_outputs="1" expect_exit_code="1" expect_failure="true">
+            <param name="study_fasta" ftype="fasta" value="study_seqs_test.fasta"/>
+            <param name="placement_tool" value="epa-ng"/>
+            <param name="min_align" value="0.10"/>
+            <conditional name="ref_dir">
+                <param name="selector" value="fungi/fungi_ITS/"/>
+            </conditional>
+            <assert_stderr>
+                <has_text text="all 5 input sequences aligned poorly to reference sequences"/>
+            </assert_stderr>
+            <assert_command>
+                <has_text text="fungi/fungi_ITS/"/>
+                <has_text text="--min_align 0.1"/>
+            </assert_command>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="study_fasta" value="study_seqs_test2.fasta"/>
+            <param name="placement_tool" value="epa-ng"/>
+            <param name="min_align" value="0.80"/>
+            <param name="intermediate_check" value="false"/>
+            <conditional name="ref_dir">
+                <param name="selector" value="custom"/>
+                <param name="custom_fna" value="img_centroid_16S_aligned_head30.fna.gz"/>
+                <param name="custom_hmm" value="img_centroid_16S_aligned_head30.hmm"/>
+                <param name="custom_tre" value="img_centroid_16S_aligned_head30.tre"/>
+                <param name="custom_model" value="img_centroid_16S_aligned_head30.model"/>
+            </conditional>
+            <output name="out_tree" ftype="newick">
+                <assert_contents>
+                    <has_text text="2511231175_test"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+            <assert_command>
+                <has_text text="custom/"/>
+            </assert_command>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Place Seqs (Sequence placement)
+===============================
+PICRUSt2 wraps HMMER to place study sequences into a reference multiple-sequence alignment and then places these sequences into the reference phylogeny with EPA-NG or SEPP. The "study sequences" referred to will be the representative OTUs and/or ASVs under the typical workflow. The tool GAPPA is used to convert the resulting .jplace object into newick format.
+
+Note
+====
+This is typically done to prepare for subsequent hidden-state prediction with PICRUSt2. Requires unaligned FASTA of study sequences. Users can specify a non-default reference files if needed.
+
+Input
+=====
+The study sequences (i.e. FASTA of amplicon sequence variants or operational taxonomic units)
+
+Output
+======
+Output tree with placed study sequences.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41587-020-0548-6</citation>
+    </citations>
+</tool>
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