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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
author iuc
date Mon, 20 Oct 2025 17:27:45 +0000
parents
children cd8c5aebb404
files gemma.xml test-data/lm_output.interval test-data/lm_output.tsv test-data/lmm_output.interval test-data/lmm_output.tsv test-data/rgenetics.bed test-data/rgenetics.bim test-data/rgenetics.fam test-data/test_kinship_matrix.tsv
diffstat 9 files changed, 302 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemma.xml	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,96 @@
+<tool id="gemma" name="GEMMA Analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
+    <description>Run association tests and kinship analysis with GEMMA</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.98.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">gemma</requirement>
+    </requirements>
+
+    <command detect_errors="aggressive"><![CDATA[
+
+ln -s '$bed.extra_files_path'/*.bed input.bed &&
+ln -s '$bed.extra_files_path'/*.bim input.bim &&
+ln -s '$bed.extra_files_path'/*.fam input.fam &&
+
+#if $lmm_inputs.analysis == "lmm"
+    gemma -bfile input -k '$lmm_inputs.kinship' -lmm 1 -o gemmarun 2>&1;
+    cp ./output/gemmarun.assoc.txt '$gemma_output';
+    awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $3, $3, $2, $4, $5, $6, $7, $8, $9, $10, $11, $12}' '$gemma_output' > '$gemma_output_int';
+#elif $lmm_inputs.analysis == "gk"
+    gemma -bfile input -gk 1 -o gemmarun 2>&1;
+    cp ./output/gemmarun.cXX.txt '$gemma_output';
+#else
+    gemma -bfile input -lm 1 -o gemmarun 2>&1;
+    cp ./output/gemmarun.assoc.txt '$gemma_output';
+    awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $3, $3, $2, $4, $5, $6, $7, $8, $9, $10, $11, $12}' '$gemma_output' > '$gemma_output_int';
+#end if
+]]> </command>
+    <inputs>
+        <param name="bed" type="data" format="pbed" label="Input PLINK dataset"/>
+        <conditional name="lmm_inputs">
+            <param name="analysis" type="select" label="Type of analysis to perform">
+                <option value="lm">Linear Model (LM)</option>
+                <option value="lmm">Linear Mixed Model (LMM)</option>
+                <option value="gk">Kinship (Genetic Relationship Matrix)</option>
+            </param>
+            <when value="lmm">
+                <param name="kinship" type="data" format="tsv,tabular" label="Kinship Matrix File" />
+            </when>
+            <when value="lm"></when>
+            <when value="gk"></when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="gemma_output" format="tsv" label="GEMMA output file"/>
+        <data name="gemma_output_int" format="interval" label="GEMMA output file interval">
+            <filter>lmm_inputs['analysis'] != 'gk'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="lmm_inputs|analysis" value="lm" />
+            <param name="bed" ftype="pbed" value="">
+                <composite_data value="rgenetics.bim"/>
+                <composite_data value="rgenetics.bed"/>
+                <composite_data value="rgenetics.fam"/>
+            </param>
+            <output name="gemma_output" file="lm_output.tsv"/>
+            <output name="gemma_output_int" file="lm_output.interval"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="lmm_inputs|analysis" value="gk" />
+            <param name="bed" ftype="pbed" value="">
+                <composite_data value="rgenetics.bim"/>
+                <composite_data value="rgenetics.bed"/>
+                <composite_data value="rgenetics.fam"/>
+            </param>
+            <output name="gemma_output" file="test_kinship_matrix.tsv"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="lmm_inputs|analysis" value="lmm" />
+            <param name="bed" ftype="pbed" value="">
+                <composite_data value="rgenetics.bim"/>
+                <composite_data value="rgenetics.bed"/>
+                <composite_data value="rgenetics.fam"/>
+            </param>
+            <param name="lmm_inputs|kinship" value="test_kinship_matrix.tsv" />
+            <output name="gemma_output" file="lmm_output.tsv"/>
+            <output name="gemma_output_int" file="lmm_output.interval"/>
+        </test>
+    </tests>
+    <help>
+
+This tool runs various GEMMA analyses. Choose from:
+- LM: Linear Model for association testing.
+- LMM: Linear Mixed Model for association testing with relatedness (requires a kinship matrix).
+- GK: Kinship calculation (genetic relationship matrix).
+    
+Provide a PLINK binary dataset as input. For LMM, also provide a precomputed kinship matrix.
+For lm/lmm analysis, the tool applies the Wald test.
+    </help>
+    <citations>
+        <citation type="doi">10.1038/ng.2310</citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lm_output.interval	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,25 @@
+chr	ps	ps	rs	n_mis	n_obs	allele1	allele0	af	beta	se	p_wald	
+22	21784722	21784722	rs2283802	0	40	4	2	0.250	0.000000e+00	1.187339e-01	1.000000e+00	
+22	21785366	21785366	rs2267000	0	40	4	2	0.438	1.360544e-02	1.036160e-01	8.962256e-01	
+22	21794754	21794754	rs16997606	0	40	1	3	0.113	1.075269e-01	1.673089e-01	5.242879e-01	
+22	21794810	21794810	rs4820537	0	40	1	3	0.412	-1.033295e-01	9.371776e-02	2.771521e-01	
+22	21797804	21797804	rs3788347	0	40	3	1	0.487	5.959476e-02	9.652065e-02	5.406336e-01	
+22	21799918	21799918	rs756632	0	40	4	2	0.113	-2.785515e-02	1.482245e-01	8.519350e-01	
+22	21807970	21807970	rs4820539	0	40	1	3	0.287	-4.754358e-02	1.115885e-01	6.724666e-01	
+22	21820335	21820335	rs2283804	0	40	1	2	0.338	1.490313e-02	1.084425e-01	8.914175e-01	
+22	21820990	21820990	rs2267006	0	40	3	1	0.338	1.490313e-02	1.084425e-01	8.914175e-01	
+22	21821000	21821000	rs4822363	0	40	4	2	0.075	-9.803922e-02	1.960784e-01	6.199583e-01	
+22	21827674	21827674	rs5751592	0	40	4	2	0.150	-1.190476e-01	1.520634e-01	4.385487e-01	
+22	21832708	21832708	rs5759608	0	40	2	4	0.450	0.000000e+00	1.003485e-01	1.000000e+00	
+22	21833170	21833170	rs5759612	0	40	3	1	0.450	0.000000e+00	1.003485e-01	1.000000e+00	
+22	21860168	21860168	rs2267009	0	40	3	4	0.250	0.000000e+00	1.187339e-01	1.000000e+00	
+22	21864366	21864366	rs2267010	0	40	3	1	0.037	9.009009e-02	2.662896e-01	7.369871e-01	
+22	21868698	21868698	rs5759636	1	39	4	2	0.051	-2.857143e-01	2.298542e-01	2.214743e-01	
+22	21871488	21871488	rs2071436	0	40	4	2	0.250	0.000000e+00	1.187339e-01	1.000000e+00	
+22	21875879	21875879	rs2267013	0	40	3	1	0.113	1.075269e-01	1.673089e-01	5.242879e-01	
+22	21889806	21889806	rs6003566	0	40	3	1	0.100	1.562500e-01	1.737709e-01	3.742237e-01	
+22	21892891	21892891	rs2256725	0	40	2	1	0.113	1.075269e-01	1.673089e-01	5.242879e-01	
+22	21896019	21896019	rs5751611	1	39	2	4	0.487	1.351351e-02	1.019659e-01	8.952646e-01	
+22	21898858	21898858	rs762601	0	40	1	3	0.362	-1.251564e-02	9.938134e-02	9.004469e-01	
+22	21899063	21899063	rs2156921	0	40	3	1	0.362	-1.251564e-02	9.938134e-02	9.004469e-01	
+22	21905642	21905642	rs4822375	0	40	1	3	0.362	-1.251564e-02	9.938134e-02	9.004469e-01	
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lm_output.tsv	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,25 @@
+chr	rs	ps	n_mis	n_obs	allele1	allele0	af	beta	se	p_wald
+22	rs2283802	21784722	0	40	4	2	0.250	0.000000e+00	1.187339e-01	1.000000e+00
+22	rs2267000	21785366	0	40	4	2	0.438	1.360544e-02	1.036160e-01	8.962256e-01
+22	rs16997606	21794754	0	40	1	3	0.113	1.075269e-01	1.673089e-01	5.242879e-01
+22	rs4820537	21794810	0	40	1	3	0.412	-1.033295e-01	9.371776e-02	2.771521e-01
+22	rs3788347	21797804	0	40	3	1	0.487	5.959476e-02	9.652065e-02	5.406336e-01
+22	rs756632	21799918	0	40	4	2	0.113	-2.785515e-02	1.482245e-01	8.519350e-01
+22	rs4820539	21807970	0	40	1	3	0.287	-4.754358e-02	1.115885e-01	6.724666e-01
+22	rs2283804	21820335	0	40	1	2	0.338	1.490313e-02	1.084425e-01	8.914175e-01
+22	rs2267006	21820990	0	40	3	1	0.338	1.490313e-02	1.084425e-01	8.914175e-01
+22	rs4822363	21821000	0	40	4	2	0.075	-9.803922e-02	1.960784e-01	6.199583e-01
+22	rs5751592	21827674	0	40	4	2	0.150	-1.190476e-01	1.520634e-01	4.385487e-01
+22	rs5759608	21832708	0	40	2	4	0.450	0.000000e+00	1.003485e-01	1.000000e+00
+22	rs5759612	21833170	0	40	3	1	0.450	0.000000e+00	1.003485e-01	1.000000e+00
+22	rs2267009	21860168	0	40	3	4	0.250	0.000000e+00	1.187339e-01	1.000000e+00
+22	rs2267010	21864366	0	40	3	1	0.037	9.009009e-02	2.662896e-01	7.369871e-01
+22	rs5759636	21868698	1	39	4	2	0.051	-2.857143e-01	2.298542e-01	2.214743e-01
+22	rs2071436	21871488	0	40	4	2	0.250	0.000000e+00	1.187339e-01	1.000000e+00
+22	rs2267013	21875879	0	40	3	1	0.113	1.075269e-01	1.673089e-01	5.242879e-01
+22	rs6003566	21889806	0	40	3	1	0.100	1.562500e-01	1.737709e-01	3.742237e-01
+22	rs2256725	21892891	0	40	2	1	0.113	1.075269e-01	1.673089e-01	5.242879e-01
+22	rs5751611	21896019	1	39	2	4	0.487	1.351351e-02	1.019659e-01	8.952646e-01
+22	rs762601	21898858	0	40	1	3	0.362	-1.251564e-02	9.938134e-02	9.004469e-01
+22	rs2156921	21899063	0	40	3	1	0.362	-1.251564e-02	9.938134e-02	9.004469e-01
+22	rs4822375	21905642	0	40	1	3	0.362	-1.251564e-02	9.938134e-02	9.004469e-01
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lmm_output.interval	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,25 @@
+chr	ps	ps	rs	n_miss	allele1	allele0	af	beta	se	logl_H1	l_remle	p_wald
+22	21784722	21784722	rs2283802	0	4	2	0.250	8.440696e-07	1.187358e-01	-2.308872e+01	1.000000e-05	9.999944e-01
+22	21785366	21785366	rs2267000	0	4	2	0.438	1.360467e-02	1.036176e-01	-2.308011e+01	1.000000e-05	8.962331e-01
+22	21794754	21794754	rs16997606	0	1	3	0.113	1.075265e-01	1.673107e-01	-2.288333e+01	1.000000e-05	5.242936e-01
+22	21794810	21794810	rs4820537	0	1	3	0.412	-1.033317e-01	9.371939e-02	-2.249042e+01	1.000000e-05	2.771503e-01
+22	21797804	21797804	rs3788347	0	3	1	0.487	5.959560e-02	9.652243e-02	-2.289906e+01	1.000000e-05	5.406353e-01
+22	21799918	21799918	rs756632	0	4	2	0.113	-2.785541e-02	1.482258e-01	-2.307108e+01	1.000000e-05	8.519350e-01
+22	21807970	21807970	rs4820539	0	1	3	0.287	-4.754444e-02	1.115898e-01	-2.299818e+01	1.000000e-05	6.724648e-01
+22	21820335	21820335	rs2283804	0	1	2	0.338	1.490395e-02	1.084443e-01	-2.307928e+01	1.000000e-05	8.914133e-01
+22	21820990	21820990	rs2267006	0	3	1	0.338	1.490395e-02	1.084443e-01	-2.307928e+01	1.000000e-05	8.914133e-01
+22	21821000	21821000	rs4822363	0	4	2	0.075	-9.803915e-02	1.960794e-01	-2.296414e+01	1.000000e-05	6.199602e-01
+22	21827674	21827674	rs5751592	0	4	2	0.150	-1.190491e-01	1.520648e-01	-2.278472e+01	1.000000e-05	4.385471e-01
+22	21832708	21832708	rs5759608	0	2	4	0.450	4.034386e-07	1.003501e-01	-2.308872e+01	1.000000e-05	9.999968e-01
+22	21833170	21833170	rs5759612	0	3	1	0.450	4.034386e-07	1.003501e-01	-2.308872e+01	1.000000e-05	9.999968e-01
+22	21860168	21860168	rs2267009	0	3	4	0.250	8.440696e-07	1.187358e-01	-2.308872e+01	1.000000e-05	9.999944e-01
+22	21864366	21864366	rs2267010	0	3	1	0.037	9.008970e-02	2.662902e-01	-2.303159e+01	1.000000e-05	7.369888e-01
+22	21868698	21868698	rs5759636	1	4	2	0.051	-2.857151e-01	2.298551e-01	-2.233148e+01	1.000000e-05	2.214746e-01
+22	21871488	21871488	rs2071436	0	4	2	0.250	8.440696e-07	1.187358e-01	-2.308872e+01	1.000000e-05	9.999944e-01
+22	21875879	21875879	rs2267013	0	3	1	0.113	1.075279e-01	1.673103e-01	-2.288332e+01	1.000000e-05	5.242873e-01
+22	21889806	21889806	rs6003566	0	3	1	0.100	1.562503e-01	1.737726e-01	-2.268872e+01	1.000000e-05	3.742274e-01
+22	21892891	21892891	rs2256725	0	2	1	0.113	1.075279e-01	1.673103e-01	-2.288332e+01	1.000000e-05	5.242873e-01
+22	21896019	21896019	rs5751611	1	2	4	0.487	1.351309e-02	1.019678e-01	-2.307994e+01	1.000000e-05	8.952698e-01
+22	21898858	21898858	rs762601	0	1	3	0.362	-1.251601e-02	9.938321e-02	-2.308079e+01	1.000000e-05	9.004459e-01
+22	21899063	21899063	rs2156921	0	3	1	0.362	-1.251601e-02	9.938321e-02	-2.308079e+01	1.000000e-05	9.004459e-01
+22	21905642	21905642	rs4822375	0	1	3	0.362	-1.251601e-02	9.938321e-02	-2.308079e+01	1.000000e-05	9.004459e-01
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/lmm_output.tsv	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,25 @@
+chr	rs	ps	n_miss	allele1	allele0	af	beta	se	logl_H1	l_remle	p_wald
+22	rs2283802	21784722	0	4	2	0.250	8.440696e-07	1.187358e-01	-2.308872e+01	1.000000e-05	9.999944e-01
+22	rs2267000	21785366	0	4	2	0.438	1.360467e-02	1.036176e-01	-2.308011e+01	1.000000e-05	8.962331e-01
+22	rs16997606	21794754	0	1	3	0.113	1.075265e-01	1.673107e-01	-2.288333e+01	1.000000e-05	5.242936e-01
+22	rs4820537	21794810	0	1	3	0.412	-1.033317e-01	9.371939e-02	-2.249042e+01	1.000000e-05	2.771503e-01
+22	rs3788347	21797804	0	3	1	0.487	5.959560e-02	9.652243e-02	-2.289906e+01	1.000000e-05	5.406353e-01
+22	rs756632	21799918	0	4	2	0.113	-2.785541e-02	1.482258e-01	-2.307108e+01	1.000000e-05	8.519350e-01
+22	rs4820539	21807970	0	1	3	0.287	-4.754444e-02	1.115898e-01	-2.299818e+01	1.000000e-05	6.724648e-01
+22	rs2283804	21820335	0	1	2	0.338	1.490395e-02	1.084443e-01	-2.307928e+01	1.000000e-05	8.914133e-01
+22	rs2267006	21820990	0	3	1	0.338	1.490395e-02	1.084443e-01	-2.307928e+01	1.000000e-05	8.914133e-01
+22	rs4822363	21821000	0	4	2	0.075	-9.803915e-02	1.960794e-01	-2.296414e+01	1.000000e-05	6.199602e-01
+22	rs5751592	21827674	0	4	2	0.150	-1.190491e-01	1.520648e-01	-2.278472e+01	1.000000e-05	4.385471e-01
+22	rs5759608	21832708	0	2	4	0.450	4.034386e-07	1.003501e-01	-2.308872e+01	1.000000e-05	9.999968e-01
+22	rs5759612	21833170	0	3	1	0.450	4.034386e-07	1.003501e-01	-2.308872e+01	1.000000e-05	9.999968e-01
+22	rs2267009	21860168	0	3	4	0.250	8.440696e-07	1.187358e-01	-2.308872e+01	1.000000e-05	9.999944e-01
+22	rs2267010	21864366	0	3	1	0.037	9.008970e-02	2.662902e-01	-2.303159e+01	1.000000e-05	7.369888e-01
+22	rs5759636	21868698	1	4	2	0.051	-2.857151e-01	2.298551e-01	-2.233148e+01	1.000000e-05	2.214746e-01
+22	rs2071436	21871488	0	4	2	0.250	8.440696e-07	1.187358e-01	-2.308872e+01	1.000000e-05	9.999944e-01
+22	rs2267013	21875879	0	3	1	0.113	1.075279e-01	1.673103e-01	-2.288332e+01	1.000000e-05	5.242873e-01
+22	rs6003566	21889806	0	3	1	0.100	1.562503e-01	1.737726e-01	-2.268872e+01	1.000000e-05	3.742274e-01
+22	rs2256725	21892891	0	2	1	0.113	1.075279e-01	1.673103e-01	-2.288332e+01	1.000000e-05	5.242873e-01
+22	rs5751611	21896019	1	2	4	0.487	1.351309e-02	1.019678e-01	-2.307994e+01	1.000000e-05	8.952698e-01
+22	rs762601	21898858	0	1	3	0.362	-1.251601e-02	9.938321e-02	-2.308079e+01	1.000000e-05	9.004459e-01
+22	rs2156921	21899063	0	3	1	0.362	-1.251601e-02	9.938321e-02	-2.308079e+01	1.000000e-05	9.004459e-01
+22	rs4822375	21905642	0	1	3	0.362	-1.251601e-02	9.938321e-02	-2.308079e+01	1.000000e-05	9.004459e-01
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgenetics.bed	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,1 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgenetics.bim	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,25 @@
+22	rs2283802	0	21784722	4	2
+22	rs2267000	0	21785366	4	2
+22	rs16997606	0	21794754	1	3
+22	rs4820537	0	21794810	1	3
+22	rs3788347	0	21797804	3	1
+22	rs756632	0	21799918	4	2
+22	rs4820539	0	21807970	1	3
+22	rs2283804	0	21820335	1	2
+22	rs2267006	0	21820990	3	1
+22	rs4822363	0	21821000	4	2
+22	rs5751592	0	21827674	4	2
+22	rs5759608	0	21832708	2	4
+22	rs5759612	0	21833170	3	1
+22	rs2267009	0	21860168	3	4
+22	rs2267010	0	21864366	3	1
+22	rs5759636	0	21868698	4	2
+22	rs2071436	0	21871488	4	2
+22	rs2267013	0	21875879	3	1
+22	rs6003566	0	21889806	3	1
+22	rs2256725	0	21892891	2	1
+22	rs12160770	0	21892925	1	3
+22	rs5751611	0	21896019	2	4
+22	rs762601	0	21898858	1	3
+22	rs2156921	0	21899063	3	1
+22	rs4822375	0	21905642	1	3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/rgenetics.fam	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,40 @@
+101 1 3 2 2 2
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+1344 1 12 13 1 1
+1344 12 0 0 1 1
+1344 13 0 0 2 1
+1345 12 0 0 1 1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_kinship_matrix.tsv	Mon Oct 20 17:27:45 2025 +0000
@@ -0,0 +1,40 @@
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