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annotate gemma.xml @ 1:cd8c5aebb404 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit d64fadb1f41a602ea4fcec8f26ab18a4f92b8c90
author iuc
date Mon, 27 Oct 2025 09:26:46 +0000
parents 14d48fd8f343
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14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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1 <tool id="gemma" name="GEMMA Analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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2 <description>Run association tests and kinship analysis with GEMMA</description>
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3 <macros>
1
cd8c5aebb404 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit d64fadb1f41a602ea4fcec8f26ab18a4f92b8c90
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4 <token name="@TOOL_VERSION@">0.98.5</token>
0
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">gemma</requirement>
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9 </requirements>
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10
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11 <command detect_errors="aggressive"><![CDATA[
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12
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13 ln -s '$bed.extra_files_path'/*.bed input.bed &&
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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14 ln -s '$bed.extra_files_path'/*.bim input.bim &&
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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15 ln -s '$bed.extra_files_path'/*.fam input.fam &&
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16
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17 #if $lmm_inputs.analysis == "lmm"
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18 gemma -bfile input -k '$lmm_inputs.kinship' -lmm 1 -o gemmarun 2>&1;
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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19 cp ./output/gemmarun.assoc.txt '$gemma_output';
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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20 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';
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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21 #elif $lmm_inputs.analysis == "gk"
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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22 gemma -bfile input -gk 1 -o gemmarun 2>&1;
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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23 cp ./output/gemmarun.cXX.txt '$gemma_output';
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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24 #else
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25 gemma -bfile input -lm 1 -o gemmarun 2>&1;
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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26 cp ./output/gemmarun.assoc.txt '$gemma_output';
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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27 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';
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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28 #end if
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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29 ]]> </command>
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30 <inputs>
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31 <param name="bed" type="data" format="pbed" label="Input PLINK dataset"/>
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32 <conditional name="lmm_inputs">
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33 <param name="analysis" type="select" label="Type of analysis to perform">
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34 <option value="lm">Linear Model (LM)</option>
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35 <option value="lmm">Linear Mixed Model (LMM)</option>
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36 <option value="gk">Kinship (Genetic Relationship Matrix)</option>
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37 </param>
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38 <when value="lmm">
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39 <param name="kinship" type="data" format="tsv,tabular" label="Kinship Matrix File" />
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40 </when>
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41 <when value="lm"></when>
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42 <when value="gk"></when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data name="gemma_output" format="tsv" label="GEMMA output file"/>
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47 <data name="gemma_output_int" format="interval" label="GEMMA output file interval">
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48 <filter>lmm_inputs['analysis'] != 'gk'</filter>
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49 </data>
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="2">
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53 <param name="lmm_inputs|analysis" value="lm" />
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54 <param name="bed" ftype="pbed" value="">
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55 <composite_data value="rgenetics.bim"/>
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56 <composite_data value="rgenetics.bed"/>
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57 <composite_data value="rgenetics.fam"/>
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58 </param>
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59 <output name="gemma_output" file="lm_output.tsv"/>
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60 <output name="gemma_output_int" file="lm_output.interval"/>
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61 </test>
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62 <test expect_num_outputs="1">
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63 <param name="lmm_inputs|analysis" value="gk" />
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64 <param name="bed" ftype="pbed" value="">
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65 <composite_data value="rgenetics.bim"/>
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66 <composite_data value="rgenetics.bed"/>
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67 <composite_data value="rgenetics.fam"/>
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68 </param>
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69 <output name="gemma_output" file="test_kinship_matrix.tsv"/>
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70 </test>
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71 <test expect_num_outputs="2">
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72 <param name="lmm_inputs|analysis" value="lmm" />
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73 <param name="bed" ftype="pbed" value="">
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74 <composite_data value="rgenetics.bim"/>
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75 <composite_data value="rgenetics.bed"/>
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76 <composite_data value="rgenetics.fam"/>
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77 </param>
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78 <param name="lmm_inputs|kinship" value="test_kinship_matrix.tsv" />
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79 <output name="gemma_output" file="lmm_output.tsv"/>
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80 <output name="gemma_output_int" file="lmm_output.interval"/>
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81 </test>
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82 </tests>
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83 <help>
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84
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85 This tool runs various GEMMA analyses. Choose from:
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86 - LM: Linear Model for association testing.
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87 - LMM: Linear Mixed Model for association testing with relatedness (requires a kinship matrix).
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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88 - GK: Kinship calculation (genetic relationship matrix).
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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89
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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90 Provide a PLINK binary dataset as input. For LMM, also provide a precomputed kinship matrix.
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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91 For lm/lmm analysis, the tool applies the Wald test.
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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92 </help>
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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93 <citations>
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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94 <citation type="doi">10.1038/ng.2310</citation>
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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95 </citations>
14d48fd8f343 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma commit cb5c00e8251af92f0b88674cdda0821cf8bdb824
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96 </tool>