[WIP] Update cd-hit to 4.8.1, add cd-hit-454, cd-hit-dup, cd-hit-lap #3328
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| <tool id="cd_hit_454" name="CD-HIT 454" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> | ||
| <description>identifies duplicates from 454 reads</description> | ||
| <macros> | ||
| <import>macros.xml</import> | ||
| </macros> | ||
| <expand macro="requirements"/> | ||
| <version_command><![CDATA[cd-hit | grep "CD-HIT version" | cut -d" " -f 4]]></version_command> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| cd-hit-454 | ||
| -i '$i' | ||
| -o 'result' | ||
| -b $b | ||
| -c $c | ||
| -n $n | ||
| -aL $aL | ||
| -AL $AL | ||
| -aS $aS | ||
| -AS $AS | ||
| $g | ||
| -D $D | ||
| -match $match | ||
| -mismatch $mismatch | ||
| -gap $gap | ||
| -gap-ext $gapext | ||
| $out.bak | ||
| -M \${GALAXY_MEMORY_MB:-0} | ||
|
There was a problem hiding this comment. Is 0 a useful default? |
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| -T \${GALAXY_SLOTS:-1} | ||
| @LOG@ | ||
| ]]></command> | ||
| <inputs> | ||
| <param argument="-i" type="data" format="fasta" label="Select file with reads"/> | ||
| <expand macro="c" default="0.98"/> | ||
| <expand macro="b" default="10"/> | ||
| <expand macro="n" default="10"/> | ||
| <expand macro="aL"/> | ||
| <expand macro="AL"/> | ||
| <expand macro="aS"/> | ||
| <expand macro="AS"/> | ||
| <expand macro="g"/> | ||
| <param argument="-D" type="integer" value="1" label="Set maximum size per indel"/> | ||
| <expand macro="match"/> | ||
| <expand macro="mismatch" default="-1"/> | ||
| <expand macro="gap" default="-3"/> | ||
| <expand macro="gapext"/> | ||
| <section name="out" title="Output options"> | ||
| <expand macro="bak"/> | ||
| <expand macro="log"/> | ||
| </section> | ||
| </inputs> | ||
| <outputs> | ||
| <expand macro="out_clusters"/> | ||
| <expand macro="out_clusters_backup"/> | ||
| <expand macro="out_sequences"/> | ||
| <expand macro="out_log"/> | ||
| </outputs> | ||
| <tests> | ||
| <!-- #1 default --> | ||
| <test expect_num_outputs="4"> | ||
| <param name="i" value="nucleotide_sequences.fasta"/> | ||
| <section name="out"> | ||
| <param name="bak" value="true"/> | ||
| <param name="log" value="true"/> | ||
| </section> | ||
| <output name="out_clusters"> | ||
| <assert_contents> | ||
| <has_n_lines n="65"/> | ||
| <has_line line=">Cluster 27"/> | ||
| <has_text_matching expression="0.+183nt.+"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_clusters_backup"> | ||
| <assert_contents> | ||
| <has_n_lines n="37"/> | ||
| <has_text_matching expression="6.+241nt"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_sequences"> | ||
| <assert_contents> | ||
| <has_n_lines n="56"/> | ||
| <has_line line=">M44Fcsw_200453"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_log"> | ||
| <assert_contents> | ||
| <has_line line="program completed !"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| <!-- #2 custom --> | ||
| <test expect_num_outputs="4"> | ||
| <param name="i" value="nucleotide_sequences.fasta"/> | ||
| <param name="c" value="0.97"/> | ||
| <param name="b" value="9"/> | ||
| <param name="n" value="11"/> | ||
| <param name="aL" value="0.9"/> | ||
| <param name="AL" value="99999998"/> | ||
| <param name="aS" value="0.9"/> | ||
| <param name="AS" value="99999998"/> | ||
| <param name="g" value="true"/> | ||
| <param name="D" value="2"/> | ||
| <param name="match" value="3"/> | ||
| <param name="mismatch" value="-2"/> | ||
| <param name="gap" value="-4"/> | ||
| <param name="gapext" value="-2"/> | ||
| <section name="out"> | ||
| <param name="bak" value="true"/> | ||
| <param name="log" value="true"/> | ||
| </section> | ||
| <output name="out_clusters"> | ||
| <assert_contents> | ||
| <has_n_lines n="60"/> | ||
| <has_line line=">Cluster 22"/> | ||
| <has_text_matching expression="0.+183nt.+"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_clusters_backup"> | ||
| <assert_contents> | ||
| <has_n_lines n="37"/> | ||
| <has_text_matching expression="3.+241nt.+"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_sequences"> | ||
| <assert_contents> | ||
| <has_n_lines n="46"/> | ||
| <has_line line=">M43Fcsw_250770"/> | ||
| </assert_contents> | ||
| </output> | ||
| <output name="out_log"> | ||
| <assert_contents> | ||
| <has_line line="program completed !"/> | ||
| </assert_contents> | ||
| </output> | ||
| </test> | ||
| </tests> | ||
| <help><![CDATA[ | ||
| .. class:: infomark | ||
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| **What it does** | ||
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| @WID@ | ||
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| *CD-HIT-454* is part of CD-HIT and identifies duplicated 454 reads by reengineering *CD-HIT-EST*. Duplicates are either exactly identical or meet these criteria: | ||
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| (1) they start at the same position | ||
| (2) their lengths can be different, but shorter one must be fully aligned with the longer one (the seed) | ||
| (3) they can only have 4% mismatches (insertion, deletion, and substitution) | ||
| (4) only 1 base is allowed per insertion or deletion | ||
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| Here, 3. and 4. can be adjusted by users. Mismatches are allowed in order to tolerate sequencing errors. Visit the `project wiki <https://github.com/weizhongli/cdhit/wiki/3.-User's-Guide#CDHIT454_clustering>`_ for a detailed description. | ||
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| **Input** | ||
|
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| Reads in FASTA format. | ||
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| **Output** | ||
|
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| - Representative sequences in FASTA format | ||
| @CLUSTER@ | ||
| @CLUSTER_BACKUP@ | ||
| - Log file | ||
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| .. class:: infomark | ||
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| **References** | ||
|
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| @REFERENCES@ | ||
| ]]></help> | ||
| <expand macro="citations"/> | ||
| </tool> | ||
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please add a recent profile
edam_topics, edam_operations and xrefs would be nice to have as well