diff sixgill_filter.xml @ 0:cf8eee8343fb draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/sixgill commit 547a3bb05a08bc4eaed224b6864a82434e09289d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sixgill_filter.xml	Thu Oct 13 08:38:04 2016 -0400
@@ -0,0 +1,120 @@
+<tool id="sixgill_filter" name="sixgill filter" version="@VERSION@.0">
+    <description>a metapeptide database</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <version_command>sixgill_filter --version</version_command>
+    <command><![CDATA[
+        sixgill_filter 
+            --nogzipout
+            --out=metapeptides_db_output.tsv
+            #if str($minorflength) != '':
+                --minorflength=$minorflength
+            #end if
+            #if str($minaaseqlength) != '':
+                --minaaseqlength=$minaaseqlength
+            #end if
+            #if str($minqualscore) != '':
+                --minqualscore=$minqualscore
+            #end if
+            #if str($minlongesttryppeplen) != '':
+                --minlongesttryppeplen=$minlongesttryppeplen
+            #end if
+            #if str($minreadcount) != '':
+                --minreadcount=$minreadcount
+            #end if
+            #if str($maxmetapeptides) != '':
+                --maxmetapeptides=$maxmetapeptides
+            #end if
+            $metapeptide_db
+            #if 'fa' in str($output_choice):
+                && sixgill_makefasta --type=aa --out="metapeptides_fa_output.fa" "metapeptides_db_output.tsv"
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="metapeptide_db" type="data" format="tabular" label="metapeptide database" 
+         help="Can be generated with sixgill_build"/>
+        <param name="minorflength" type="integer" value="40" min="0" optional="true" label="minorflength"
+                help="min length of ORF-portion"/>
+        <param name="minaaseqlength" type="integer" value="10" min="0" optional="true" label="minaaseqlength"
+                help="min AA sequence length"/>
+        <param name="minqualscore" type="integer" value="30" min="0" optional="true" label="minqualscore"
+                help="min base-call phred score across any NT in a metapeptide"/>
+        <param name="minlongesttryppeplen" type="integer" value="7" min="0" optional="true" label="minlongesttryppeplen"
+                help="minimum length of the longest tryptic peptide"/>
+        <param name="minreadcount" type="integer" value="2" min="1" optional="true" label="minreadcount"
+                help="minimum read count"/>
+        <param name="minmetagenescore" type="integer" value="" min="-1" optional="true" label="minmetagenescore"
+                help="minimum MetaGene score"/>
+        <param name="maxmetapeptides" type="integer" value="" optional="true" label="maxmetapeptides"
+                help="maximum number of metapeptides to write"/>
+        <param name="output_choice" type="select" multiple="true" optional="false" label="select outputs">
+            <option value="db" selected="true">metapeptide database</option>
+            <option value="fa">metapeptide protein fasta</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_db" format="tabular" label="${tool.name} on ${on_string}: metapeptides.tsv" from_work_dir="metapeptides_db_output.tsv">
+            <filter>'db' in output_choice</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="sequence,length,min_qualscore,partial_orf_length,metagene_score,read_ids" />
+            </actions>
+        </data>
+        <data name="output_fa" format="fasta" label="${tool.name} on ${on_string}: metapeptides.fa" from_work_dir="metapeptides_fa_output.fa">
+            <filter>'fa' in output_choice</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="metapeptide_db" ftype="tabular" value="metagene_nometagene_merged.metapeptides.tsv"/>
+            <param name="minreadcount" value="2"/>
+            <param name="minaaseqlength" value="12"/>
+            <param name="output_choice" value="db"/>
+            <output name="output_db">
+                <assert_contents>
+                    <has_text text="DLRILLRERLVAGDSDEAAVDFIVDR" />
+                    <not_has_text text="YHNFEGYRWR" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+usage: sixgill_filter [-h] --out OUT [--minorflength MINORFLENGTH]
+                      [--minaaseqlength MINAASEQLENGTH]
+                      [--minreadcount MINREADCOUNT]
+                      [--minqualscore MINQUALSCORE]
+                      [--minlongesttryppeplen MINLONGESTTRYPPEPLEN]
+                      [--minmetagenescore MINMETAGENESCORE]
+                      [--maxmetapeptides MAXMETAPEPTIDES] [--debug]
+                      metapeptidefile
+
+Filter a metapeptide database.
+
+positional arguments:
+  metapeptidefile       input metapeptide database file
+
+optional arguments:
+  -h, --help            show this help message and exit
+  --out OUT             output metapeptide database file
+  --minorflength MINORFLENGTH
+                        minimum ORF length
+  --minaaseqlength MINAASEQLENGTH
+                        minimum AA sequence length
+  --minreadcount MINREADCOUNT
+                        minimum read count
+  --minqualscore MINQUALSCORE
+                        minimum basecall quality
+  --minlongesttryppeplen MINLONGESTTRYPPEPLEN
+                        minimum length of the longest tryptic peptide
+  --minmetagenescore MINMETAGENESCORE
+                        Minimum MetaGene score (-1 for none)
+  --maxmetapeptides MAXMETAPEPTIDES
+                        maximum number of metapeptides to write
+  --debug               Enable debug logging
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>