diff macros.xml @ 0:678260997e94 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/muon/ commit bcf2ec32c3d13b29da55e0e638da7ddd7162c436

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Feb 05 10:53:25 2025 +0000
@@ -0,0 +1,264 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">muon</requirement>
+            <requirement type="package" version="0.10.2">leidenalg</requirement>
+            <requirement type="package" version="0.8.2">louvain</requirement>
+            <requirement type="package" version="0.7.2">mofapy2</requirement>
+        </requirements>
+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">muon</xref>
+        </xrefs>
+    </xml>
+    <xml name="creators">
+        <creator>
+            <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
+        </creator>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1186/s13059-021-02577-8</citation>
+        </citations>
+    </xml>
+    <xml name="sanitize_query">
+        <sanitizer>
+            <valid initial="string.printable">
+                <remove value="&apos;" />
+            </valid>
+       </sanitizer>
+    </xml>
+    <xml name="sanitize_string">
+        <sanitizer>
+            <valid initial="string.letters,string.digits"><add value="_" /></valid>
+        </sanitizer>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[python -c "import muon as mu;print('Muon version: %s' % mu.__version__)"]]></version_command>
+    </xml>
+
+    <token name="@CMD_imports@"><![CDATA[
+import mudata as md
+import muon as mu
+import scanpy as sc
+import os
+            ]]>
+    </token>
+    <xml name="inputs_mudata">
+        <param name="mdata" type="data" format="h5ad" label="MuData input file"/>
+    </xml>
+    <token name="@CMD_read_inputs@"><![CDATA[
+mdata = md.read('mudata.h5mu')
+        ]]>
+    </token>
+    <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|MuData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g"  | sed -r 's|^\s*(.*):\s(.*)|[\1]\n-    \2|g' | sed 's|, |\n-    |g'
+    ]]></token>
+    <token name="@COPY_MUDATA@"><![CDATA[
+cp '$mdata' 'mudata.h5mu' &&
+    ]]>
+    </token>
+
+    <token name="@CMD@"><![CDATA[
+cat '$script_file' > '$hidden_output' &&
+python '$script_file' >> '$hidden_output' &&
+touch 'mudata_info.txt' &&
+cat 'mudata_info.txt' @CMD_prettify_stdout@
+    ]]>
+    </token>
+
+    <token name="@CMD_params_clustering@"><![CDATA[
+    #if $method.res.type == 'same'
+        #if str($method.res.resolution)
+    resolution=$method.res.resolution,
+        #end if
+    #else if $method.res.type == 'separate'
+    resolution={
+        #for $modality in $method.res.modalities
+        '$modality.mod_name': $modality.resolution,
+        #end for
+    },
+    #end if
+    #if $method.weights.type == 'same'
+        #if str($method.weights.mod_weights)
+    mod_weights=$method.weights.mod_weights,
+        #end if
+    #else if $method.weights.type == 'separate'
+    mod_weights={
+        #for $modality in $method.weights.modalities
+        '$modality.mod_name': $modality.mod_weights,
+        #end for
+    },
+    #end if
+    random_state=$method.random_state,
+    key_added='$method.key_added',
+    #if $method.neighbors_key
+    neighbors_key='$method.neighbors_key',
+    #end if
+    directed=$method.directed
+    ]]></token>
+
+    <token name="@CMD_neighbor_keys@"><![CDATA[
+    #if $method.n_keys.type == 'same'
+    neighbor_keys='$method.n_keys.neighbor_keys',
+    #else if $method.n_keys.type == 'separate'
+    neighbor_keys={
+        #for $modality in $method.n_keys.modalities
+        '$modality.mod_name': '$modality.neighbor_keys',
+        #end for
+    },
+    #end if
+    ]]></token>
+    <token name="@CMD_params_embedding@"><![CDATA[
+    #if $method.color
+    #set $color = ([x.strip() for x in str($method.color).split(',')])
+    color=$color,
+    #end if
+    use_raw=$method.use_raw,
+    #if $method.layer
+    layer='$method.layer',
+    #end if
+    ]]></token>
+
+    <xml name="inputs_common_advanced">
+        <section name="advanced_common" title="Advanced Options" expanded="false">
+            <param name="show_log" type="boolean" checked="false" label="Output Log?" />
+        </section>
+    </xml>
+    <xml name="outputs_common_advanced">
+        <data name="hidden_output" format="txt" label="Log file" >
+            <filter>advanced_common['show_log']</filter>
+        </data>
+    </xml>
+    <xml name="muon_outputs">
+        <data name="mudata_out" format="h5ad" from_work_dir="mudata.h5mu" label="${tool.name} (${method.method}) on ${on_string}: MuData"/>
+        <expand macro="outputs_common_advanced"/>
+    </xml>
+    <token name="@CMD_mudata_write_outputs@"><![CDATA[
+mdata.write('mudata.h5mu')
+with open('mudata_info.txt','w', encoding='utf-8') as ainfo:
+    print(mdata, file=ainfo)
+        ]]>
+    </token>
+
+    <xml name="param_neighbor_keys">
+        <conditional name="n_keys">
+            <param name="type" type="select" label="Same or separate neighborhood information for each modality?">
+                <option value="same">Same neighborhood key for all modalities</option>
+                <option value="separate">Separate neighborhood keys per modality</option>
+            </param>
+            <when value="same">
+                <param argument="neighbor_keys" type="text" value="neighbors" label="Keys in .uns where per-modality neighborhood information is stored"/>
+            </when>
+            <when value="separate">
+                <repeat name="modalities" title="Modalities" min="2" default="2">
+                    <param name="mod_name" type="text" label="Modality name" optional="true">
+                        <expand macro="sanitize_string" />
+                    </param>
+                    <param argument="neighbor_keys" type="text" value="neighbors" label="Keys in .uns where neighborhood information is stored"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_resolution">
+        <conditional name="res">
+            <param name="type" type="select" label="Same or separate resolutions for each modality?">
+                <option value="same">Same resolution for all modalities</option>
+                <option value="separate">Separate resolutions per modality</option>
+            </param>
+            <when value="same">
+                <param argument="resolution" type="float" optional="true" label="Coarseness of the clustering" help="Higher values -> more clusters"/>
+            </when>
+            <when value="separate">
+                <repeat name="modalities" title="Modalities" min="2" default="2">
+                    <param name="mod_name" type="text" label="Modality name" optional="true">
+                        <expand macro="sanitize_string" />
+                    </param>
+                    <param name="resolution" type="float" label="Resolution for the above modality" help="Higher values -> more clusters"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_weight">
+        <conditional name="weights">
+            <param name="type" type="select" label="Same or separate weights for each modality?">
+                <option value="same">Same weight for all modalities</option>
+                <option value="separate">Separate weight per modality</option>
+            </param>
+            <when value="same">
+                <param argument="mod_weights" type="float" optional="true" label="Weight each modality controlling its contribution" help="Higher values -> more important"/>
+            </when>
+            <when value="separate">
+                <repeat name="modalities" title="Modalities" min="2" default="2">
+                    <param name="mod_name" type="text" label="Modality name" optional="true">
+                        <expand macro="sanitize_string" />
+                    </param>
+                    <param name="mod_weights" type="float" label="Weight for the above modality" help="Higher values -> more important"/>
+                </repeat>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_random_state" tokens="seed">
+        <param argument="random_state" type="integer" value="@SEED@" optional="true" label="Random seed for the optimization"/>
+    </xml>
+    <xml name="param_key_added" tokens="key_added">
+        <param argument="key_added" type="text" value="@KEY_ADDED@" label="mdata.obs key where cluster labels to be added">
+            <expand macro="sanitize_string" />
+        </param>
+    </xml>
+    <xml name="param_neighbors_key">
+        <param argument="neighbors_key" type="text" optional="true" label="Use neighbors connectivities as adjacency"
+        help="If not specified, look for .obsp['connectivities'] in each modality.
+        If specified, look for .obsp[.uns[neighbors_key]['connectivities_key']] in each modality for connectivities.">
+            <expand macro="sanitize_string" />
+        </param>
+    </xml>
+    <xml name="param_directed">
+        <param argument="directed" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Treat the graph as directed"/>
+    </xml>
+    <xml name="param_key_added_common">
+        <param argument="key_added" type="text" optional="true" label="Key to be added to store neighbors, distances and connectivities data"
+            help="If not specified, the multimodal neighbors data is stored in .uns['neighbors'], distances and connectivities are stored in .obsp['distances'] and .obsp['connectivities'], respectively.
+            If specified, the neighbors data is added to .uns[key_added], distances are stored in .obsp[key_added + '_distances'] and connectivities in .obsp[key_added + '_connectivities'].">
+            <expand macro="sanitize_string" />
+        </param>
+    </xml>
+    <xml name="param_eps" tokens="eps_value">
+        <param argument="eps" type="float" value="@EPS_VALUE@" label="Small number to avoid numerical errors"/>
+    </xml>
+    <xml name="param_use_raw" tokens="label,checked">
+        <param argument="use_raw" type="boolean" truevalue="True" falsevalue="False" checked="@CHECKED@" label="@LABEL@" />
+    </xml>
+    <xml name="param_keys">
+        <conditional name="key_variables">
+            <param name="type" type="select" label="Keys to plot">
+                <option value="var_names">All variables in '.var_names'</option>
+                <option value="obs">All fields in '.obs'</option>
+                <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
+            </param>
+            <when value="var_names"/>
+            <when value="obs"/>
+            <when value="custom">
+                <param argument="keys" type="text" value="" label="Keys to plot" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
+                    <expand macro="sanitize_query" />
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="param_color">
+        <param argument="color" type="text" optional="true" label="Keys for variables or annotations of observations (.obs columns)" help="Can be from any modality.">
+            <expand macro="sanitize_query" />
+        </param>
+    </xml>
+    <xml name="params_embedding">
+        <expand macro="param_color"/>
+        <expand macro="param_use_raw" label="Use raw slot of AnnData as input values" checked="true"/>
+        <param argument="layer" type="text" optional="true" label="Name of the layer in the modality where a feature (from color) is derived from"
+            help="If a valid layer is provided, this takes precedence over use_raw=True">
+            <expand macro="sanitize_query" />
+        </param>
+    </xml>
+</macros>