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diff deseq2_visualisation_macros.xml @ 0:6507a8d42a4f draft default tip

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planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a
author frogs
date Wed, 04 Feb 2026 13:16:44 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq2_visualisation_macros.xml	Wed Feb 04 13:16:44 2026 +0000
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+<?xml version="1.0"?>
+<macros>
+    <token name="@DESEQ2_ASV_VISUALISATION_CMD_LINE@">
+        deseq2_visualisation.py
+            --analysis-type 'ASV'
+            --phyloseq-rdata '$phyloseq_rdata' 
+            --deseq-rdata '$deseq_rdata'
+            --var-exp '$var_exp'
+            #if $varType.vartType_selected == "qualitative":
+                --mod1 '$varType.mod1' 
+                --mod2 '$varType.mod2'
+            #end if
+            --padj $padj
+            --html '$html'
+    </token>
+
+    <xml name="deseq2_asv_visualisation_inputs">
+        <!-- Files -->
+        <param argument="--phyloseq-rdata" type="data" format="rdata" label="Phyloseq object (.Rdata)" help="Rdata file generated by the FROGS Stat Phyloseq import for ASV data."/>
+        <param argument="--deseq-rdata" type="data" format="rdata" label="DESeq2 object (.Rdata)" help="Rdata file generated by the FROGS Stat DESeq2 Preprocess tool for ASV data."/>
+        <!-- Parameters -->
+        <param argument="--var-exp" type="text" label="Experimental variable" help="Sample metadata variable expected to influence ASV abundances (e.g., Treatment, Site, Environment, etc.).">
+            <expand macro="restricted_sanitizer_validator"/>
+        </param>
+        <conditional name="varType">
+            <param name="vartType_selected" type="select" label="Is the experimental variable quantitative or qualitative?" help="Select whether the experimental variable is qualitative (categorical) or quantitative (numerical). If qualitative, specify two conditions to compare.">
+                <option value="qualitative">Qualitative</option>
+                <option value="quantitative">Quantitative</option>
+            </param>
+            <when value="qualitative">
+                <param argument="--mod2" type="text"  label="Condition 1 considered as reference" help="Condition used as reference in the comparison (e.g., Control, Untreated, With).">
+                   <expand macro="restricted_sanitizer_validator"/>
+                </param>
+                <param argument="--mod1" type="text"  label="Condition 2 to be compared to the reference" help="Condition to compare against the reference (e.g., Treated, Without).">
+                   <expand macro="restricted_sanitizer_validator"/>
+                </param>
+            </when>
+            <when value="quantitative"/>
+        </conditional>
+        <param argument="--padj" type="float" value="0.05" label="Adjusted p-value threshold" help="Adjusted p-value cutoff used to determine significantly differentially abundant ASVs (default: 0.05)."/>
+    </xml>
+
+    <!-- Test -->
+    <xml name="deseq2_asv_visualisation_test_input">
+        <param name="phyloseq_rdata" value="references/16-phylo_import.Rdata" />
+        <param name="deseq_rdata" value="references/23-deseq2_preprocess_asv.Rdata"/>
+        <param name="var_exp" value="EnvType" />
+        <conditional name="varType">
+            <param name="vartType_selected" value="qualitative"/>
+            <param name="mod1" value="BoeufHache"/>
+            <param name="mod2" value="SaumonFume"/>
+        </conditional>
+        <param name="padj" value="0.05" />
+    </xml>
+
+    <xml name="deseq2_asv_visualisation_test_output">
+        <output name="html" count="1">
+            <assert_contents>
+                <!-- HTML size or line diff can't be used as many information about path, os, date are present. -->
+                <!-- Here we test only title, intermediate results and output of last R command -->
+				<!-- Deseq2 is influenced by other intermediate libraries or packages and results are hard to compare -->
+                <has_text text="Stat: DESeq2 Visualisation" />
+                <has_text text="(deseq2_visualisation.py" />
+				<has_text text="v5.1.0)" />
+                <has_text text='["otu_01582",' />
+                <!-- baseMean value of otu_01582 -->
+                <has_text text='[52.4455' />
+                <!-- Log2 FC of otu_01582 -->
+                <has_text text='[21.6623' />
+                <!-- lfcSE of otu_01582 -->
+                <has_text text='[2.2089' />
+                <has_text text='─ Session info ───────────────────────────────────────────────────────────────' />
+            </assert_contents>
+        </output>
+    </xml>
+
+    <token name="@DESEQ2_FUN_VISUALISATION_CMD_LINE@">
+        deseq2_visualisation.py
+            --analysis 'FUNCTION'
+            --phyloseq-rdata '$phyloseq_rdata' 
+            --deseq-rdata '$deseq_rdata'
+            --var-exp '$var_exp'
+            #if $varType.vartType_selected == "qualitative":
+                --mod1 '$varType.mod1' 
+                --mod2 '$varType.mod2'
+            #end if
+            --padj $padj
+            --html '$html'
+            --output-ipath-over '$Function_over_abund'
+            --output-ipath-under '$Function_under_abund'
+    </token>
+
+    <xml name="deseq2_fun_visualisation_inputs">
+        <!-- Files -->
+        <param argument="--phyloseq-rdata" type="data" format="rdata" label="Phyloseq object (.Rdata)" help="Rdata file generated by the FROGS Stat DESeq2 Preprocess analysis for FUNCTION data."/>
+        <param argument="--deseq-rdata" type="data" format="rdata" label="DESeq2 object (.Rdata)" help="Rdata file generated by the FROGS Stat DESeq2 Preprocess analysis for FUNCTION data."/>
+        <!-- Parameters -->
+        <param argument="--var-exp" type="text" label="Experimental variable" help="Sample metadata variable expected to influence functional abundances (e.g., Treatment, Site, Environment, etc.).">
+            <expand macro="restricted_sanitizer_validator"/>
+        </param>
+        <conditional name="varType">
+            <param name="vartType_selected" type="select" label="Is the experimental variable quantitative or qualitative?" help="Select whether the experimental variable is qualitative (categorical) or quantitative (numerical). If qualitative, specify two conditions to compare.">
+                <option value="qualitative">Qualitative</option>
+                <option value="quantitative">Quantitative</option>
+            </param>
+            <when value="qualitative">
+                <param argument="--mod2" type="text"  label="Condition 1 considered as reference" help="Condition used as reference in the comparison (e.g., Control, Untreated, With).">
+                   <expand macro="restricted_sanitizer_validator"/>
+                </param>
+                <param argument="--mod1" type="text"  label="Condition 2 to be compared to the reference" help="Condition to compare against the reference (e.g., Treated, Without).">
+                   <expand macro="restricted_sanitizer_validator"/>
+                </param>
+            </when>
+            <when value="quantitative"/>
+        </conditional>
+        <param argument="--padj" type="float" value="0.05" label="Adjusted p-value threshold" help="Adjusted p-value cutoff used to determine significantly differentially abundant functions (default: 0.05)."/>
+    </xml>
+
+    <!-- Test -->
+    <xml name="deseq2_fun_visualisation_test_input">
+        <param name="phyloseq_rdata" value="references/23-phyloseq_functions.Rdata" />
+        <param name="deseq_rdata" value="references/23-deseq2_preprocess_func.Rdata"/>
+        <param name="var_exp" value="EnvType" />
+        <conditional name="varType">
+            <param name="vartType_selected" value="qualitative"/>
+            <param name="mod1" value="BoeufHache"/>
+            <param name="mod2" value="SaumonFume"/>
+        </conditional>
+        <param name="padj" value="0.05" />
+    </xml>
+
+    <xml name="deseq2_fun_visualisation_test_output">
+        <output name="html" count="1">
+            <assert_contents>
+                <!-- HTML size or line diff can't be used as many information about path, os, date are present. -->
+                <!-- Here we test only title, intermediate results and output of last R command -->
+                <has_text text="Stat: DESeq2 Visualisation" />
+                <has_text text="(deseq2_visualisation.py v5.1.0)" />
+                <has_text text='["EC:1.3.1.76",' />
+                <!-- baseMean value of EC:1.3.1.76 -->
+                <has_text text='[753.1103444315089' />
+                <!-- Log2 FC of EC:1.3.1.76 -->
+                <has_text text='[-8.386170731613163' />
+                <!-- lfcSE of EC:1.3.1.76 -->
+                <has_text text='[1.005359955086068' />
+                <!-- pvalue EC:1.3.1.76 -->
+                <has_text text='[7.337830601151377e-17' />
+                <has_text text='─ Session info ───────────────────────────────────────────────────────────────' />
+            </assert_contents>
+        </output>
+    </xml>
+</macros>