diff cmsearch-deoverlap.xml @ 0:54b16c794341 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap commit 675c458c910bb85bd472e25209fa1df43179efb6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmsearch-deoverlap.xml	Sat Aug 19 05:37:02 2023 +0000
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+<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy0" profile="21.05">
+    <description>removes lower scoring overlaps from cmsearch results</description>
+    <requirements>
+        <requirement type="package" version="5.26">perl</requirement>
+    </requirements>
+    <command><![CDATA[
+        ln -s '$clan_information' clan_info &&
+        ln -s '$cmsearch_matches' cmsearch_matches &&
+        LC_ALL=C perl '$__tool_directory__/cmsearch-deoverlap.pl'
+        --clanin clan_info cmsearch_matches
+        #if $maxkeep:
+            $maxkeep
+        #end if
+        #if $dirty:
+            $dirty &&
+            mv *.sort '$matches_sort'
+        #end if
+        &&
+        mv *.deoverlapped '$deoverlapped_matches'
+
+    ]]></command>
+    <inputs>
+        <param name="clan_information" type="data" format="txt" label="Clan information" help="Each row in the file contains an RNA clan and its corresponding family members"/>
+        <param name="cmsearch_matches" type="data" format="tabular" label="The tabular result file from cmsearch"/>
+        <param argument="--maxkeep" type="boolean" truevalue="--maxkeep" falsevalue="" label="Keep hits that only overlap with other hits that are not kept" help="If this option is not set, all hits with higher scoring overlap will be removed." />
+        <param argument="--dirty" type="boolean" truevalue="--dirty" falsevalue="" label="Keep the intermediate sorted tblout file"/>
+    </inputs>
+    <outputs>
+        <data name="deoverlapped_matches" format="tabular" label="Deoverlapped matches" />
+        <data name="matches_sort" format="tabular" label="Sorted matches">
+            <filter>dirty</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="clan_information" value="ribo.claninfo" />
+            <param name="cmsearch_matches" value="1.cmsearch.tblout" />
+            <param name="dirty" value="--dirty"/>
+            <output name="deoverlapped_matches" file="1.cmsearch.tblout.deoverlapped" />
+            <output name="matches_sort" file="1.cmsearch.tblout.sort" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="clan_information" value="ribo.claninfo" />
+            <param name="cmsearch_matches" value="1.cmsearch.tblout" />
+            <param name="dirty" value=""/>
+            <output name="deoverlapped_matches" file="1.cmsearch.tblout.deoverlapped" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What this tool does**
+
+This tool removes lower-scoring overlaps from cmsearch results. Given information about the clans and the cmsearch tbl output this tool returns a filtered cmsearch tbl output.
+
+**clan.info:**
+
+CL00111	SSU_rRNA_bacteria SSU_rRNA_archaea SSU_rRNA_eukarya SSU_rRNA_microsporidia SSU_trypano_mito
+
+CL00112	LSU_rRNA_archaea LSU_rRNA_bacteria LSU_rRNA_eukarya LSU_trypano_mito 5_8S_rRNA
+
+CL99999 5S_rRNA mtPerm-5S
+
+**cmsearch.tblout:**
+
+contig--2249925      -         SSU_rRNA_bacteria    RF00177   hmm       19      914        2      898      +     -    6 0.50   5.7  638.4  1.1e-189 !   -
+
+contig--2255364      -         SSU_rRNA_bacteria    RF00177   hmm      325     1084      765        1      -     -    6 0.52   3.9  624.0  2.5e-185 !   -
+
+contig--2369838      -         SSU_rRNA_bacteria    RF00177   hmm       90      938       20      855      +     -    6 0.52   7.0  609.3  6.6e-181 !   -
+
+contig--2271497      -         SSU_rRNA_bacteria    RF00177   hmm        4      812      835        2      -     -    6 0.51   5.0  597.5  2.5e-177 !   -
+
+contig--2369838      -         SSU_rRNA_archaea     RF01959   hmm       70      894       17      855      +     -    6 0.52   5.4  346.7  9.9e-102 !   -
+
+**cmsearch.tblout.deoverlapped:**
+
+contig--2249925      -         SSU_rRNA_bacteria    RF00177   hmm       19      914        2      898      +     -    6 0.50   5.7  638.4  1.1e-189 !   -
+
+contig--2255364      -         SSU_rRNA_bacteria    RF00177   hmm      325     1084      765        1      -     -    6 0.52   3.9  624.0  2.5e-185 !   -
+
+contig--2271497      -         SSU_rRNA_bacteria    RF00177   hmm        4      812      835        2      -     -    6 0.51   5.0  597.5  2.5e-177 !   -
+
+contig--2369838      -         SSU_rRNA_bacteria    RF00177   hmm       90      938       20      855      +     -    6 0.52   7.0  609.3  6.6e-181 !   -
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @software{nawrocki_nawrockiecmsearch_tblout_deoverlap_2019,
+	        title = {nawrockie/cmsearch\_tblout\_deoverlap},
+	        url = {https://github.com/nawrockie/cmsearch_tblout_deoverlap},
+	        abstract = {Script that removes lower scoring overlaps from cmsearch v1.1x --tblout files.},
+	        author = {Nawrocki, Eric},
+	        year = {2019}}
+        </citation>
+    </citations>
+</tool>