--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Oct 12 07:43:59 2022 +0000
@@ -0,0 +1,188 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.7.2</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.01</token>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">medaka</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
+            <yield />
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>medaka --version</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{medaka,
+              author = {Oxford Nanopore Technologies Ltd.},
+              title = {medaka},
+              year = 2020,
+              url = {https://github.com/nanoporetech/medaka},
+              urldate = {2020-05-06}
+            }</citation>
+        </citations>
+    </xml>
+
+    <!--
+        command
+    -->
+
+    <token name="@REF_FASTA@"><![CDATA[
+        #if $reference_source.reference_source_selector == 'history':
+            #if $reference_source.ref_file.ext.endswith(".gz")
+                gunzip -c '$reference_source.ref_file' > reference.fa &&
+            #else
+                ln -f -s '$reference_source.ref_file' reference.fa &&
+            #end if
+        #else:
+            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
+        #end if
+    ]]></token>
+
+    <!--
+        input
+    -->
+
+    <xml name="b" token_argument="-b">
+        <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
+    </xml>
+    <xml name="model" token_argument="-m" token_label="Select model">
+        <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model, 
+            according to the basecaller used. Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION 
+            or PromethION), iii) the basecaller variant, and iv) the basecaller version">
+            <option value="r103_fast_g507">r103_fast_g507</option>
+            <option value="r103_fast_snp_g507">r103_fast_snp_g507</option>
+            <option value="r103_fast_variant_g507">r103_fast_variant_g507</option>
+            <option value="r103_hac_g507">r103_hac_g507</option>
+            <option value="r103_hac_snp_g507">r103_hac_snp_g507</option>
+            <option value="r103_hac_variant_g507">r103_hac_variant_g507</option>
+            <option value="r103_min_high_g345">r103_min_high_g345</option>
+            <option value="r103_min_high_g360">r103_min_high_g360</option>
+            <option value="r103_prom_high_g360">r103_prom_high_g360</option>
+            <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
+            <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
+            <option value="r103_sup_g507">r103_sup_g507</option>
+            <option value="r103_sup_snp_g507">r103_sup_snp_g507</option>
+            <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
+            <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
+            <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
+            <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
+            <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
+            <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
+            <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option>
+            <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
+            <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
+            <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</option>
+            <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
+            <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
+            <option value="r104_e81_sup_g610">r104_e81_sup_g610</option>
+            <option value="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>            
+            <option value="r10_min_high_g303">r10_min_high_g303</option>
+            <option value="r10_min_high_g340">r10_min_high_g340</option>   
+            <option value="r941_e81_fast_variant_g514">r941_e81_fast_variant_g514</option>
+            <option value="r941_e81_hac_g514">r941_e81_hac_g514</option>
+            <option value="r941_e81_hac_variant_g514">r941_e81_hac_variant_g514</option>
+            <option value="r941_e81_sup_g514">r941_e81_sup_g514</option>
+            <option value="r941_e81_sup_variant_g514">r941_e81_sup_variant_g514</option>
+            <option value="r941_min_fast_g303">r941_min_fast_g303</option>
+            <option value="r941_min_fast_g507">r941_min_fast_g507</option>
+            <option value="r941_min_fast_snp_g507">r941_min_fast_snp_g507</option>
+            <option value="r941_min_fast_variant_g507">r941_min_fast_variant_g507</option>
+            <option value="r941_min_hac_g507">r941_min_hac_g507</option>
+            <option value="r941_min_hac_snp_g507">r941_min_hac_snp_g507</option>
+            <option value="r941_min_hac_variant_g507">r941_min_hac_variant_g507</option>
+            <option value="r941_min_high_g303">r941_min_high_g303</option>
+            <option value="r941_min_high_g330">r941_min_high_g330</option>
+            <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
+            <option value="r941_min_high_g344">r941_min_high_g344</option>
+            <option value="r941_min_high_g351">r941_min_high_g351</option>
+            <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
+            <option value="r941_min_sup_g507">r941_min_sup_g507</option>
+            <option value="r941_min_sup_snp_g507">r941_min_sup_snp_g507</option>
+            <option value="r941_min_sup_variant_g507">r941_min_sup_variant_g507</option>
+            <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
+            <option value="r941_prom_fast_g507">r941_prom_fast_g507</option>
+            <option value="r941_prom_fast_snp_g507">r941_prom_fast_snp_g507</option>
+            <option value="r941_prom_fast_variant_g507">r941_prom_fast_variant_g507</option>
+            <option value="r941_prom_hac_g507">r941_prom_hac_g507</option>
+            <option value="r941_prom_hac_snp_g507">r941_prom_hac_snp_g507</option>
+            <option value="r941_prom_hac_variant_g507">r941_prom_hac_variant_g507</option>
+            <option value="r941_prom_high_g303">r941_prom_high_g303</option>
+            <option value="r941_prom_high_g330">r941_prom_high_g330</option>
+            <option value="r941_prom_high_g344">r941_prom_high_g344</option>
+            <option value="r941_prom_high_g360">r941_prom_high_g360</option>
+            <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
+            <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
+            <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
+            <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
+            <option value="r941_prom_sup_g507">r941_prom_sup_g507</option>
+            <option value="r941_prom_sup_snp_g507">r941_prom_sup_snp_g507</option>
+            <option value="r941_prom_sup_variant_g507">r941_prom_sup_variant_g507</option>
+            <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
+            <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
+            <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
+            <option value="r941_sup_plant_g610">r941_sup_plant_g610</option>
+            <option value="r941_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
+        </param>
+    </xml>
+    <xml name="reference">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <when value="cached">
+                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No reference genomes are available"/>
+                    </options>
+                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+                </param>
+            </when>
+            <when value="history">
+                <param name="ref_file" type="data" format="fasta,fasta.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
+            </when>
+        </conditional>
+    </xml>
+
+    <!--
+        Help
+    -->
+
+    <token name="@WID@"><![CDATA[
+*medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
+
+This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
+    ]]></token>
+
+    <token name="@MODELS@"><![CDATA[
+
+----
+
+.. class:: infomark
+
+**Models**
+
+For best results it is important to specify the correct model, -m in the above, according to the basecaller used. Allowed values can be found by running medaka tools list\_models.
+
+Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the basecaller variant, and iv) the basecaller version, with the format:
+
+    ::
+
+        {pore}_{device}_{caller variant}_{caller version}
+
+For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model 
+r941_prom_hac_g303 should be used with PromethION data and the high accuracy basecaller (termed "hac" in Guppy configuration files). Where a version of Guppy has been used without an exactly corresponding medaka model, the medaka model with the highest version equal to or less than the guppy version should be selected.
+          
+    ]]></token>
+
+    <token name="@REFERENCES@"><![CDATA[
+More information are available in the `manual <https://github.com/nanoporetech/medaka/tree/master/docs>`_ and `github <https://github.com/nanoporetech/medaka>`_.
+    ]]></token>
+</macros>