diff missing_values_sample_filter.xml @ 0:91441e41cc3d draft

"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 6321871098b2c4bc9e321d20b7e66fff3d641839"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/missing_values_sample_filter.xml	Sat Apr 11 16:47:00 2020 -0400
@@ -0,0 +1,110 @@
+<tool id="dimspy_missing_values_sample_filter" name="Missing Values Sample Filter" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
+    <description> - Remove samples with a high percentage of missing values</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        dimspy mv-sample-filter
+        --input '$hdf5_file_in'
+        --output '$hdf5_file_out'
+        --max-fraction $max_fraction
+        &&
+        dimspy create-sample-list
+        --input '$hdf5_file_out'
+        --output '$samplelist'
+        --delimiter tab
+        #if $hdf5_to_txt.standard
+            &&
+            @HDF5_PM_TO_TXT@
+        #end if
+        #if $hdf5_to_txt.comprehensive
+            &&
+            @HDF5_PM_TO_TXT_COMPREHENSIVE@
+        #end if
+    ]]>
+    </command>
+    <inputs>
+        <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peak Intensity Matrix (HDF5 file)" help="" />
+        <param name="max_fraction" argument="--max-fraction" type="float" min="0" max="1.0" value="0.8" label="Maximum percentage of missing values." help="" />
+        <param name="delimiter" argument="--delimiter" type="hidden" value="tab" label="" help=""/>
+        <expand macro="hdf5_pm_to_txt" />
+    </inputs>
+    <outputs>
+        <expand macro="outputs_peak_intensity_matrix" />
+        <data name="samplelist" format="tsv" label="${tool.name} on ${on_string}: Sample Metadata (updated)" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="hdf5_file_in" value="pm_as_bf_sf.h5" ftype="h5"/>
+            <param name="max_fraction" value="0.8"/>
+            <param name="delimiter" value="tab"/>
+            <conditional name="hdf5_to_txt">
+                <param name="standard" value="True"/>
+                <param name="comprehensive" value="False"/>
+                <param name="representation_samples" value="rows"/>
+                <param name="matrix_attr" value="intensity"/>
+            </conditional>
+            <output name="hdf5_file_out" file="pm_as_bf_sf_mv.h5" ftype="h5" compare="sim_size"/>
+            <output name="matrix_file_out" file="peak_matrix_as_bf_sf_mv.txt" ftype="tsv"/>
+            <output name="samplelist" file="sample_list_after_mv_filter.txt" ftype="tsv"/>
+        </test>
+    </tests>
+    <help>
+----------------------------
+Missing Values Sample Filter
+----------------------------
+
+..
+
+---------------------------------------------
+
+Description
+-----------
+
+Standard DIMS processing workflow: Process Scans -> Replicate Filter -> Align Samples -> **[Missing values sample filter]** -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics
+
+|
+
+This tool is used to remove study samples with greater-than a user-defined “Maximum percentage of missing values” from the peak intensity matrix. A missing value is defined as the absence of a recorded peak intensity value for a specific mass spectral peak, in a specific study sample.
+
+Samples with large numbers of missing values are often observed where a failed mass spectral acquisition has occurred, the reasons for which are many and diverse.
+
+---------------------------------------------
+
+Parameters
+----------
+
+**Peak Intensity Matrix (HDF5 file)** (REQUIRED) - for routine usage, the input peak intensity matrix should be that generated from the 'Align samples' tool.
+
+**Maximum percentage of missing values** (REQUIRED; default = 0.8) - a numeric value ranging from 0 to 1 (decimal representation of percentage), where:
+
+    - A value of 0 (i.e. 0%) corresponds to a very harsh filtering procedure, in which only those samples with zero missing values are retained in the output peak matrix.
+    
+    - A value of 1 (i.e. 100%) corresponds to a very liberal filtering procedure, in which samples with as many as 100% missing values will be retained in the output peak matrix.
+
+|
+
+@help_options_addtional_output@
+
+|
+
+---------------------------------------------
+
+Output file(s)
+--------------
+
+**IMPORTANT** - in all outputs except for the (optional) comprehensive output, if a sample had greater-than the user defined maximum percentage of missing values, then this sample is removed from the output peak matrix.
+
+
+@help_outputs_matrix@
+
+---------------------------------------------
+
+@github_developers_contributors@
+@license@
+    </help>
+    <expand macro="citations" />
+</tool>
+