diff fast5_subset.xml @ 0:0fbeff566070 draft default tip

"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/ont_fast5_api commit 9fb27995131a4106053eb85d687857d2cbd2a5c6"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fast5_subset.xml	Sat May 22 15:11:43 2021 +0000
@@ -0,0 +1,112 @@
+<?xml version="1.0"?>
+<tool id="ont_fast5_api_fast5_subset" name="@TOOL_NAME@ Subset" version="@TOOL_VERSION@+galaxy2" profile="18.01">
+    <description>of multi read file(s)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <!-- no specific version command for subcommand fast5_subset available -->
+    <version_command><![CDATA[compress_fast5 -v]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+## initialize
+mkdir -p './data' &&
+tar -xf '$input' -C './data' &&
+
+## run
+fast5_subset
+--recursive
+## required
+--input './data'
+@SAVEPATH@
+--read_id_list '$read_id_list'
+## optional
+@COMPRESSION@
+@BATCHSIZE@
+@THREADS@
+
+## create tarball
+@TARBALL@
+    ]]></command>
+    <inputs>
+        <expand macro="input" argument="--input"/>
+        <param argument="--read_id_list" type="data" format="txt,tabular" label="Select file with read IDs" help="Either containing 1 read_id per line or a tabular file with a column named read_id."/>
+        <expand macro="batch_size"/>
+        <expand macro="compression"/>
+    </inputs>
+    <outputs>
+        <expand macro="output"/>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="2">
+            <param name="input" value="multi.fast5.tar"/>
+            <param name="read_id_list" value="list.txt"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="30720"/>
+                </assert_contents>
+            </output>
+            <output name="summary" ftype="txt" value="filename_mapping_1.txt" compare="sim_size" delta="1" />
+        </test>
+        <!-- #2 -->
+        <test expect_num_outputs="2">
+            <param name="input" value="multi.fast5.tar"/>
+            <param name="read_id_list" value="list.txt"/>
+            <param name="batch_size" value="2"/>
+            <param name="compression" value="gzip"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="51200"/>
+                </assert_contents>
+            </output>
+            <output name="summary" ftype="txt" value="filename_mapping_2.txt" compare="sim_size" delta="1" />
+        </test>
+        <!-- #3 -->
+        <test expect_num_outputs="2">
+            <param name="input" value="multi.fast5.tar"/>
+            <param name="read_id_list" value="list.txt"/>
+            <param name="compression" value="vbz"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="40960"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #4 -->
+        <test expect_num_outputs="2">
+            <param name="input" value="multi.fast5.tar"/>
+            <param name="read_id_list" value="list.txt"/>
+            <param name="compression" value="vbz_legacy_v0"/>
+            <output name="out_results">
+                <assert_contents>
+                    <has_size value="40960"/>
+                </assert_contents>
+            </output>
+            <output name="summary" ftype="txt" value="filename_mapping_4.txt" compare="sim_size" delta="1" />
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+*fast5_subset* extracts reads from multi read FAST5 file(s) based on a list of read IDs.
+
+**Input**
+
+Multi read file(s) in FAST5 format, that are stored in a flat TAR, and a list of read IDs that should be extracted.
+
+**Output**
+
+Multi read file(s) in FAST5 format containing a subset of the input file(s). The rseults are are stored in a flat TAR.
+
+.. class:: infomark
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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