Mercurial > repos > iuc > codeml
changeset 4:682e5eca7458 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/codeml commit 6ecdbaa25d4cad3580baa17853ef546b6f975628"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 09:54:56 +0000 |
| parents | 96806adbb000 |
| children | |
| files | codeml.xml macros.xml test-data/1_codeml.ctl test-data/2_codeml.ctl test-data/3_codeml.ctl |
| diffstat | 5 files changed, 38 insertions(+), 38 deletions(-) [+] |
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--- a/codeml.xml Wed Sep 16 16:45:37 2020 +0000 +++ b/codeml.xml Sat Nov 27 09:54:56 2021 +0000 @@ -1,4 +1,4 @@ -<tool name="codeML" id="codeml" version="@WRAPPER_VERSION@+galaxy1" profile="18.01"> +<tool name="codeML" id="codeml" version="@TOOL_VERSION@+galaxy2" profile="18.01"> <description> Detects positive selection (paml package) </description> @@ -8,7 +8,7 @@ </macros> <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">paml</requirement> + <requirement type="package" version="@TOOL_VERSION@">paml</requirement> </requirements> <version_command><![CDATA[ codeml /dev/null 2>&1 | tail -1 ]]></version_command> @@ -56,7 +56,7 @@ ncatG = $adv.ncatG * # of categories in dG of NSsites models fix_rho = $adv.fix_rho * 0: estimate rho; 1: fix it at rho rho = $adv.rho * initial or fixed rho, 0:no correlation - getSE = $adv.getSE * 0: don't want them, 1: want S.E.s of estimates + getSE = $adv.getSE * 0: dont want them, 1: want S.E.s of estimates RateAncestor = $adv.RateAncestor * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) Small_Diff = $adv.Small_Diff cleandata = $adv.cleandata * remove sites with ambiguity data (1:yes, 0:no)? @@ -238,13 +238,13 @@ <outputs> <data format="txt" name="ctl" label="${tool.name} on ${on_string}: codeml.ctl" /> - <data format="txt" name="2ngdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" > + <data format="txt" name="twongdn" from_work_dir="2NG.dN" label="${tool.name} on ${on_string}: 2NG.dN" > <filter>adv['seqtype']=="1"</filter> </data> - <data format="txt" name="2ngds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" > + <data format="txt" name="twongds" from_work_dir="2NG.dS" label="${tool.name} on ${on_string}: 2NG.dS" > <filter>adv['seqtype']=="1"</filter> </data> - <data format="txt" name="2ngt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" > + <data format="txt" name="twongt" from_work_dir="2NG.t" label="${tool.name} on ${on_string}: 2NG.t" > <filter>adv['seqtype']=="1"</filter> </data> <data format="txt" name="lnf" from_work_dir="lnf" label="${tool.name} on ${on_string}: lnf"/> @@ -252,25 +252,25 @@ <data format="txt" name="rst1" from_work_dir="rst1" label="${tool.name} on ${on_string}: rst1"/> <data format="txt" name="rub" from_work_dir="rub" label="${tool.name} on ${on_string}: rub"/> <data format="txt" name="run" from_work_dir="run_codeml" label="${tool.name} on ${on_string}: run_codeml"/> - <data format="txt" name="4fold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc"> + <data format="txt" name="fourfold" from_work_dir="4fold.nuc" label="${tool.name} on ${on_string}: 4fold.nuc"> <filter>adv['verbose']=="1"</filter> </data> </outputs> <tests> - <test> + <test expect_num_outputs="9"> <conditional name="compat_model" > <param name="brmodel" value="0" /> <param name="NSsites" value="0" /> </conditional> - <param name="adv.fix_omega" value="0" /> - <param name="adv.omega" value="0.2" /> + <param name="adv|fix_omega" value="0" /> + <param name="adv|omega" value="0.2" /> <param name="RateAncestor" value="1" /> <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> - <param name="tree" ftype="txt" value="RAxML_bestTree" /> - <output name="2ngdn" value="1_2ngdn" /> - <output name="2ngds" value="1_2ngds" /> - <output name="2ngt" value="1_2ngt" /> + <param name="tree" value="RAxML_bestTree" ftype="nhx" /> + <output name="twongdn" value="1_2ngdn" /> + <output name="twongds" value="1_2ngds" /> + <output name="twongt" value="1_2ngt" /> <output name="run"> <assert_contents> <has_text text="CODONML (in paml version 4.9, March 2015)"/> @@ -279,19 +279,19 @@ </output> <output name="ctl" value="1_codeml.ctl" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="9"> <conditional name="compat_model" > <param name="brmodel" value="2" /> <param name="NSsites" value="0" /> </conditional> - <param name="adv.fix_omega" value="0" /> - <param name="adv.omega" value="0.2" /> + <param name="adv|fix_omega" value="0" /> + <param name="adv|omega" value="0.2" /> <param name="RateAncestor" value="1" /> <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> - <param name="tree" ftype="txt" value="tree_model2" /> - <output name="2ngdn" value="2_2ngdn" /> - <output name="2ngds" value="2_2ngds" /> - <output name="2ngt" value="2_2ngt" /> + <param name="tree" value="tree_model2" ftype="nhx" /> + <output name="twongdn" value="2_2ngdn" /> + <output name="twongds" value="2_2ngds" /> + <output name="twongt" value="2_2ngt" /> <output name="run"> <assert_contents> <has_text text="CODONML (in paml version 4.9, March 2015)"/> @@ -300,19 +300,19 @@ </output> <output name="ctl" value="2_codeml.ctl" lines_diff="4" /> </test> - <test> + <test expect_num_outputs="9"> <conditional name="compat_model" > <param name="brmodel" value="3" /> <param name="NSsites" value="2" /> </conditional> - <param name="adv.fix_omega" value="0" /> - <param name="adv.omega" value="0.2" /> + <param name="adv|fix_omega" value="0" /> + <param name="adv|omega" value="0.2" /> <param name="RateAncestor" value="1" /> <param name="concat_nuc" ftype="fasta" value="concat.fasta" /> - <param name="tree" ftype="txt" value="tree_model3" /> - <output name="2ngdn" value="3_2ngdn" /> - <output name="2ngds" value="3_2ngds" /> - <output name="2ngt" value="3_2ngt" /> + <param name="tree" value="tree_model3" ftype="nhx" /> + <output name="twongdn" value="3_2ngdn" /> + <output name="twongds" value="3_2ngds" /> + <output name="twongt" value="3_2ngt" /> <output name="run"> <assert_contents> <has_text text="CODONML (in paml version 4.9, March 2015)"/>
--- a/macros.xml Wed Sep 16 16:45:37 2020 +0000 +++ b/macros.xml Sat Nov 27 09:54:56 2021 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@WRAPPER_VERSION@">4.9</token> + <token name="@TOOL_VERSION@">4.9</token> <xml name="FSsites_br0" > <param argument="NSsites" type="select" label="Site model ; fix_alpha !=1 and alpha !=0 are not compatible with NSsites !=0" > <option value="0" selected="true">0 : e.g. basic model if model=0</option>
--- a/test-data/1_codeml.ctl Wed Sep 16 16:45:37 2020 +0000 +++ b/test-data/1_codeml.ctl Sat Nov 27 09:54:56 2021 +0000 @@ -1,7 +1,7 @@ - seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_1.dat * sequence data file name + seqfile = /tmp/tmpag83k3gw/files/2/a/5/dataset_2a51ed5b-9c83-455a-bcf6-3f83c1505ff8.dat * sequence data file name outfile = run_codeml * main result file name - treefile = /tmp/tmpr0j4bmyj/files/000/dataset_2.dat * tree structure file name + treefile = /tmp/tmpag83k3gw/files/e/1/9/dataset_e195971f-e59d-4e2c-8b36-ab81d32476dc.dat * tree structure file name noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 0 * 1: detailed output, 0: concise output runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic @@ -35,7 +35,7 @@ ncatG = 3 * # of categories in dG of NSsites models fix_rho = 1 * 0: estimate rho; 1: fix it at rho rho = 0.0 * initial or fixed rho, 0:no correlation - getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + getSE = 0 * 0: dont want them, 1: want S.E.s of estimates RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) Small_Diff = 5e-07 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
--- a/test-data/2_codeml.ctl Wed Sep 16 16:45:37 2020 +0000 +++ b/test-data/2_codeml.ctl Sat Nov 27 09:54:56 2021 +0000 @@ -1,7 +1,7 @@ - seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_12.dat * sequence data file name + seqfile = /tmp/tmpag83k3gw/files/2/6/2/dataset_262fd0d9-9018-4668-992c-0ed4943f9168.dat * sequence data file name outfile = run_codeml * main result file name - treefile = /tmp/tmpr0j4bmyj/files/000/dataset_13.dat * tree structure file name + treefile = /tmp/tmpag83k3gw/files/c/2/b/dataset_c2b7d4a1-033d-4bd9-92ba-ad7936f0c09a.dat * tree structure file name noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 0 * 1: detailed output, 0: concise output runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic @@ -35,7 +35,7 @@ ncatG = 3 * # of categories in dG of NSsites models fix_rho = 1 * 0: estimate rho; 1: fix it at rho rho = 0.0 * initial or fixed rho, 0:no correlation - getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + getSE = 0 * 0: dont want them, 1: want S.E.s of estimates RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) Small_Diff = 5e-07 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
--- a/test-data/3_codeml.ctl Wed Sep 16 16:45:37 2020 +0000 +++ b/test-data/3_codeml.ctl Sat Nov 27 09:54:56 2021 +0000 @@ -1,7 +1,7 @@ - seqfile = /tmp/tmpr0j4bmyj/files/000/dataset_23.dat * sequence data file name + seqfile = /tmp/tmpag83k3gw/files/9/9/6/dataset_99661b4e-1dc8-471d-9db3-6eb3d2655fbe.dat * sequence data file name outfile = run_codeml * main result file name - treefile = /tmp/tmpr0j4bmyj/files/000/dataset_24.dat * tree structure file name + treefile = /tmp/tmpag83k3gw/files/d/4/d/dataset_d4d2b602-4042-48d7-9636-abdf169513fa.dat * tree structure file name noisy = 9 * 0,1,2,3,9: how much rubbish on the screen verbose = 0 * 1: detailed output, 0: concise output runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic @@ -35,7 +35,7 @@ ncatG = 3 * # of categories in dG of NSsites models fix_rho = 1 * 0: estimate rho; 1: fix it at rho rho = 0.0 * initial or fixed rho, 0:no correlation - getSE = 0 * 0: don't want them, 1: want S.E.s of estimates + getSE = 0 * 0: dont want them, 1: want S.E.s of estimates RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states (1 or 2) Small_Diff = 5e-07 cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?